Studies of Bacterial Chemotaxis Using Microfluidics - Interview

My name is Roman Stocker. I'm a second year assistant professor in the Ralph Parsons Laboratory, which is part of the Department of Civil and Environmental Engineering here at MIT. I'm originally from Italy and I studied fluid mechanics.

My background is therefore more in the physical sciences, but in the past two years, three years actually, I've moved more into environmental and biological topics. Two years ago, I've started developing microfluidics to look at problems in microbial ecology and using these micro devices, we are able to develop typical ecological questions for things at the scales of microns. Our work is primarily concerned with al organisms, those that can swim around in the ocean and track their sources of food.

In particular, bacteria have developed very clever ways of swimming, and I have a small demonstration here. The bacterial head is pretty much an ellipsoid. You imagine this being about two microns in size.

At the back of the bacterium, there is one or more flagella. These flagella are helical structures, which the bacterium can rot rotate. That rotation pro produces trust that allows the bacterium to actually swim forward.

There is different modes in which bacteria actually do that, and there are different strategies of swimming and it is part of what our research is concerned with. The reason bacteria swim in the ocean is to be able to better exploit sources of nutrients, and that is part of a paradigm shift which has occurred over the last 15 or 20 years. Before that, people used to think that the ocean was a homogeneous soup of nutrients at scales of meters and up to tens of meters, and in that picture of the ocean, these small scale organisms like bacteria were taught to play no substantial role and they were really just passively vectored by the oceanic occurrence.

But 10 or 15 years ago, people realized that that is really not what is going on in the ocean and that in fact these small scale organisms are among the most important players in determining the ocean health and therefore even things like our global climate. This is so because of two reasons. The first reason is that they occur everywhere in the ocean and their cumulative biomass by far exceeds that of all other marine organisms.

The second reason, and maybe the most fundamental one, is that these small scale organisms by utilizing nutrient sources and in particular carbon, can recycle the nutrients for other components of the food web and therefore substantially intensifying other aspects and other parts of the trophic chain in the ocean. In all of this, our work focuses primarily on interaction between swimming organisms and nutrient patches. Bacteria not only are able to swim, but they also able to sense detect nutrient gradients.

That is, they're able to tell when life is getting better and swim up gradients of nutrients. They do that in a process known as a chemotaxis.Properly. Chemo taxes is the ability to sense a chemical gradient and by swimming home in on it.

This is really what we study in the lab and microfluidics is a tool that allows us to probe the chemotactic and swimming abilities of bacteria and therefore extrapolate and scale up their role to determine how important they are in the determining the health of the ocean. In the Past year and a half, we've set up micro devices that allow us to expose bacteria to different kind of conditions that you typically find in the ocean. As I said earlier, typical nutrient patches, but also for example, turbulence.

The what we have found so far is that marine bacteria seem to have adapted very efficiently to exploit these nutrient patches and to be able to counteract by swimming a large variety of conditions of turbulence conditions in the ocean that would make them very well suited to actually survive in an ocean, which is typically a desert of nutrients from their point of view and in which nutrients occur only in scattered and very rare patches in a three-dimensional water column, and at the same time be able to swim, to fight turbulence and therefore still be able to track their nutrient foods even when the water around them is moving violently. The Earth system initiative is a very interesting initiative and one that brings together a variety of people from different disciplines, all interested in understanding better how our planet actually works. In short, the earth system initiative's goal is to try to do the same thing for the planet as we are already doing and have been doing for a long time.

For the human body that is understanding its health, understanding the health of the planet these days is particularly important because of concerns of global warming, for example, and greenhouse gases and several of the efforts within the earth system initiative are geared towards understanding the health of the planet better. Our work fits into that by looking at one component of the carbon cycle in the ocean. We try to understand in particular how small scale organisms, as I mentioned earlier, swimming bacteria in particular can affect these large scale cycles, which has repercussions on the global carbon cycle in the ocean and therefore on the global carbon cycle worldwide, including the Atmosphere.

All of our work So far in this field has been allowed and actually triggered by one key technological advance, and that is microfluidics. In the past 10 years, microfluidics has been developed into a really interesting and cool tool in particular in the Boston Cambridge area. The originator of the microfluidics technology in its current form is Professor George Whitesides at Harvard who introduced the process of soft lithography and the use of PDMS for micro devices fabrication.

Since then, the application of microfluidics has grown exponentially in a whole range of fields. From chemical engineering to the health sciences, we have started applying it to microbial ecology and to address some of these small scale problems in in the ocean regarding the swimming of microorganisms. In a nutshell, it is difficult, if not impossible to study these processes directly in the ocean because of their small scales and because of the variability that the ocean necessarily presents, we are still not able to visualize bacteria which are about a micron in size, directly in situ in the ocean, and at the same time, people have tried to model these processes, for example, numerically or theoretically, but because this is biology, you necessarily have to rely on assumptions.

For example, you will have to make assumptions about the swimming strategy of a bacteria or the chemo taxi strategy of a bacterium, and therefore real experiments are needed to make progress in this field. Microfluidics allows us to take small regions, small parts of the ocean into the lab, and at the same time expose bacteria and microorganisms to environmental conditions that are realistic, both in terms of nutrients and in terms of flows. At the same time, by using video microscopy and cell tracking, we can study the behavior of individual bacteria in a very carefully controlled manner that allows us to make progress in these questions in a way that would not have been possible about 10 years ago, and all of that is due to technological advances, specifically micro Verdicts.

There are two main challenges I see lying ahead of us in this field. The first one, as I mentioned earlier, is to be able at some point to take these questions to the ocean. The reason that one ultimately needs to go to the ocean is to capture all the variability that is inherent in these processes.

For example, we still have no idea of what really leaks out of a settling particle, what kind of nutrients are present, what kind of chemical compounds do bacteria chemo tax towards in the lab. We can only study the simplest of these conditions, but what really occurs in the ocean is a collection of complicated and very variable processes that we need to ultimately explore direct directly in C two. This is a big challenge from the point of view of sampling from a point of view of imaging and from the point of view of doing chemical and biological analysis on scales, which as I mentioned a few times are only in the order of a few micrometers and in terms of volumes of picoliters.

The second challenge that I see more easier to tackle is that visualizing behavior in three dimensions. Everything we do currently in the lab is two dimensional. We use conventional microscopy to visualize trajectories and accumulation of microorganisms, but we have great hope in a technique known as digital holography for giving us in the timeframe of maybe three to five years the ability to track these things in three dimensions and therefore more fatefully and more realistically, realistically be able to capture the ecology In the next Five years.

In addition to trying to go three dimensional in the sampling and perhaps trying to make the first, first naive steps possibly towards the sampling things in the ocean, we definitely want to link these studies with ongoing efforts to understand genomics of these organisms. There is a big push in particular as part of the earth system initiative in understanding the genetic composition and the variability in terms of genetics of these bacteria out there in the field. At the same time, genomics lacks the ability of directly linking the findings with the behavior of the organisms, and that is what we hope that microfluidics and these more behavioral, classical ecological studies will be able to bring to the table.

We have a great setup and a great team of people looking at the genomics of marine bacteria, and by collaborating with them, we hope to be able to link these two fundamental questions to get a better understanding of what bacteria out there in the ocean and what their role is in determining the health of the ocean and health of the planet.