How do bacteria make decisions? Part 1.

PALM image, chemotaxis, azospirillum brasilense, <span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft_id=info%3Adoi%2F10.1371%2Fjournal.pbio.1000137&rft.atitle=Self-Organization+of+the+Escherichia+coli+Chemotaxis+Network+Imaged+with+Super-Resolution+Light+Microscopy.&rft.jtitle=PLoS+Biology&rft.volume=7&rft.issue=6&rft.spage=e1000137&;bpr3.tags=Research+%2F+Scholarship">Greenfield D. & et al  (2009). Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy., <span style="font-style:italic;">PLoS Biology, 7</span> (6) e1000137. DOI: <a rel="author" href="">10.1371/journal.pbio.1000137</a></span>
This beautiful figure shows where different chemotaxis proteins are found within an E. coli cell at stunning resolution. From Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, et al. (2009) Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy. PLoS Biol 7(6): e1000137. doi:10.1371/journal.pbio.1000137

Yes. You read the title correctly. Decision making is not limited to animals like humans or birds. Bacteria also make decisions with intricate precision. Imagine being so tiny that you are literally moved by water molecules bumping into you. This is what bacteria encounter perpetually. Now, imagine having no eyes, no ears, no sense of touch, no taste or nose. How would you know what or who was around you? How would you find food now as compared to where you were a short time ago? This is where being able to sense important things like a food source is critical. Bacteria have this on their “mind” all the time. Depending on the size of a bacterium’s genome, these tiny organisms have the ability to sense hundreds to thousands of internal and external signals like carbon sources, nitrogen sources, and pH changes. If these bacteria are motile (able to move around), they can compare how conditions are for them now against how they were a few seconds ago. That’s right, bacteria have a memory albeit short. If conditions are better, they can continue to move in a forward direction. If conditions are worse compared to a few seconds earlier, they can change direction and continue searching for better conditions in their environment to generate energy. But, how do they decide?

I will focus on a lesser known bacterium as my example since I have the most knowledge about it. Azospirillum brasilense is found in the soil around the world and interacts with the roots of cereal plants like corn and wheat. A. brasilense is almost always (except when attached to plant roots) motile and searching for the best niche to provide energy for the cell. This bacterium can “make” its own usable form of nitrogen from nitrogen gas in the air through a process known as nitrogen fixation. This costs the cell a lot of energy so they are searching for nitrogen sources as well as the necessary carbon sources for life. The microscopic world can be cut throat. Having the ability to sense a greater variety of food compounds could mean the difference between being the predominant species in town or being on the fringe.

Back to the question about how these cells decide which direction to travel. One way is through a dedicated group of proteins that regulate how often the cell switches direction. This group of proteins control chemotaxis, the movement of a cell in response to chemicals within their environment. The number of chemotaxis genes varies depending on the complexity of metabolism for a bacterium. The champion at the moment is 129 from Pseudomonas syringae pv. oryzae str. 1_6. The proteins that actually sense the chemical signal are called methyl-accepting chemotaxis proteins (MCPs) or chemoreceptors. Azosprillum brasilense has 48 MCPs within its genome. This does not mean, however, that A. brasilense cells can only sense 48 different chemicals. Most, but not all, of these MCPs don’t interact with the chemicals themselves but sense the changes in the amount of energy the cell has within the environment they reside. If things are good, the MCPs are inactive. However, if energy levels are lower than they were a few seconds before, the MCPs become active and begin the signal to change direction. And these MCPs are VERY sensitive to changes. For example, if the A. brasilense cells are swimming in a liquid medium with 1,000 molecules of sugar, they will detect changes of addition or removal of a few sugar molecules in the medium. Now, move these cells immediately into a medium with 1,000,000,000,0000 sugar molecules and they still will be able to detect removal or addition of a few sugar molecules. This is called adaptation and allows the cells to remain sensitive no matter the concentrations of compounds they encounter.

In Part 2, we will talk about what happens next in the decision making process of bacteria.

<span title=”ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft_id=info%3Adoi%2F10.1371%2Fjournal.pbio.1000137&rft.atitle=Self-Organization+of+the+Escherichia+coli+Chemotaxis+Network+Imaged+with+Super-Resolution+Light+Microscopy.&rft.jtitle=PLoS+Biology&rft.volume=7&rft.issue=6&rft.spage=e1000137&;bpr3.tags=Research+%2F+Scholarship”>Greenfield D. & et al  (2009). Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy., <span style=”font-style:italic;”>PLoS Biology, 7</span> (6) e1000137. DOI: <a rel=”author” href=”″>10.1371/journal.pbio.1000137</a></span>

MyTH: Week 3 bacterial species is Caulobacter crescentus

This is a physical model of a bacterial flagel...
This is a physical model of a bacterial flagellum. It was imaged and modeled at Brandeis University in the DeRosier lab and printed at the University of Wisconsin – Madison. It was fabricated on a ZCorp Z406 printer from a VRML generated at Brandeis. (Photo credit: Wikipedia)
Caulobacter crescentus
Caulobacter crescentus (Photo credit: Microbe World)

It’s time again for the weekly My Tiny Highlight (MyTH). This week we will explore one of my favorites, Caulobacter crescentus. C. crescentus is a unique bacterium that has made it the focus of a lot of research due to its lifestyle and easy observable changes in cell shape. Part of the C. crescentus life cycle is spent freely swimming in its aquatic habitat using a single flagellum. These are called swimmer cells. At some point in development, the swimmer cell ejects the flagellum from itself and begins growing a stalk on the opposite cell pole as the flagellum. As the stalk continues growing, the cell produces a VERY stickly glue called holdfast at the tip of the stalk which is used to attach to a surface and is called a stalked cell. The cell undergoes division assymetrically; meaning, the two daughter cells produced are not identical (as is the case for most bacteria). One daughter becomes a swimmer cell due to new flagellum synthesis on one pole while the other remains stalked.

Thinking about split personality, how can one cell contain both a flagellum and a stalk simultaneously; both being functional? This is the focus of years of research. One answer refers to my favorite molecule discussed in earlier MyTH posts, the bacterial second messenger cyclic-di-GMP. Cyclic-di-GMP is constantly being made and degraded in C. crescentus. However, the production and degradation are sequestered to opposite poles of the cell via precise protein localization. The enzyme needed to produce c-di-GMP is at the stalked pole while the enzyme to degrade c-di-GMP is at the swimmer pole. Although there are no physical compartments within this bacterial cell, the concentration of c-di-GMP is not uniform throughout. The proteins that interact with c-di-GMP are predominantly at the stalked pole and allow for the stalk to elongate and leave the flagellated pole alone. Brilliant!




C. crescentus is also of importance for its ability to clean up contaminated surface and subsurface groundwater because it is resistant to the effects of heavy metal exposure. Also, examination of the genome was used to determine the ancestry of C. crescentus. It contains gene clusters similar to Pseudomonas species and others that are predominantly found in the soil. This fact along with the presence of genes necessary to breakdown plant-derived carbon molecules suggests C. crescentus originated on land (or under it) before winding up in its present day niche.

English: Graphical representation of Caulobacter crescentus (Photo credit: Wikipedia)

MyTH: Week 2 bacteria focus organism: Azospirillum brasilense

Welcome to week two of My Tiny Highlight (MyTH). This week I will focus my attention on a bacterium not many people know about, Azospirillum brasilense or A. brasilense. I know quite a bit about this one since it was the model organism used for my dissertation (sorry, under embargo…no link). The genus Azospirillum is found in almost all soils across the globe. A. brasilense, as you may be able to decipher from its name, was discovered in Brazil and is found associated with roots of different cereals (wheat, corn, even rice). Like most bacteria, A. brasilense is good to have around. It was thought for a long time that this organism provided the plants it colonizes with a usable form of nitrogen since A. brasilense is able to fix nitrogen (turn nitrogen gas found in the atmosphere into useful ammonium). However, A. brasilense is greedy and has two ways to uptake ammonium into the cell if it happens to leak out somehow. So how is A. brasilense beneficial to a plant?

Glad you asked. Azospirilla have the capacity to produce plant hormones, specifically auxins. Auxins are a class of plant hormones derived from the amino acid tryptophan. In plants, among other things, auxins increase nutrient uptake. More nutrients for the plant means increased plant growth and by consequence more nutrients and growth for A. brasilense. So, instead of increasing its own nutrient uptake (which increases the need for energy to be spent), A. brasilense ‘tricks’ the plant into doing it by just producing plant hormones. Brilliant!

The auxin indoleacetic acid
The auxin indoleacetic acid (Photo credit: Wikipedia)

Wait…it gets better. Maybe you have heard of quorum sensing (check here). Bacteria produce and release a chemical signal that is recognized by other cells and gives them instructions (go away or come here and settle down). Some recent research (personal observation) suggests auxins are quorum signals in A. brasilense telling other cells to come join in and settle down. Since A. brasilense is almost always motile, moving around in search of the best environment for the cell, a signal telling these cells to stop is amazing.


tlp1 pRKdeltapilZ 6


Picture of A. brasilense colony on agar plant and not color enhanced. They actually are pink/orange from production of carotenoids.

Azospirillum brasilense


Electron micrograph of A. brasilense.

Watch short movie of A. brasilense swimming in liquid media Here

One amazing behavior in A. brasilense is a phenomenon called aerotaxis. It is similar to chemotaxis, the movement of cells along gradients of a chemical. However, as you might predict, aerotaxis is movement of a cell long a gradient of air. A. brasilense prefer an environment with a low oxygen concentration (~0.4% compared to atmospheric oxygen concentration of 21%). From the meniscus, they will form a thin band of cells at the concentration of oxygen they like in a small capillary filled with liquid (see below).

Azospirillum brasilense capillary aerotaxis


Image of A. brasilense cells in a small glass capillary. A aerotactic band of cells (whitish in color) forms a certain distance from the meniscus (left side of image).



This is all I can provide at this time. I may update this post at a later time. Hope you enjoy the MyTH series! Next week, I will highlight one of my personal favorites. Stay tuned!


Wanted: A Nation of Bill Nyes. Making science mainstream, fun, and relevant. Part 4. « Taking Science to the People

Wanted: A Nation of Bill Nyes. Making science mainstream, fun, and relevant. Part 4. « Taking Science to the People

In my humble opinion, keeping a child’s curiosity and imagination alive is a major step towards having real progress in attitudes and participation in STEM education. I personally wanted to be a doctor growing up. I was fascinated with how all cell types worked together. The checks and balances. As I grew older, in came the question of what specialty to go into as a medical professional. Knowing my interests, it seemed no ‘specialty’ was specialized enough. Then while working at a summer internship at the Oak Ridge National Laboratory, I went into an office with the Biochemical Pathways wall poster.
I could not take my eyes off of this masterpiece. To me, this poster symbolized life at the smallest scale but yet so sophisticated and precise; not to mention the signal transduction pathways that mediate the pathways output at any given time. I had found my calling. This visualization of what I had been taught in biology classes at all levels and biochem classes in college came to fruition.
For others, I’m sure it is different and I’m sure it’s not for everyone. The goal, inspire as many as possible to explore their curiosity of how life works and how they could make it better. Now the question, how do we do it?