Another animated GIF: growing iron oxide on Geobacter pili: bacterial nanowires

bacterial nanowire, bacteria, chemotaxis, microbiology, geobacter
A bacterial nanowire. Electrons (yellow) are passed through pili (purple) to OmcS (cyan) for reduction of iron (black).

Bacteria Chemotaxis Explained with Animated GIFs. Bacterial Behavior in Motion

bacteria, chemotaxis, random bias
With no attractant or repellant, bacteria have a “random bias”. This means they switch direction randomly.
bacteria, chemotaxis, attractant response
When bacteria are in an attractant gradient (colored orange), they switch direction less often when attractant concentration is higher.
bacteria, chemotaxis, repellant response
However, when a repellant is present (colored red), bacteria switch direction more often in high repellant concentrations.

 

 

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&rft.date=2009&rfr_id=info%3Asid%2Fscienceseeker.org&rft.au=Greenfield+Derek&rft.aulast=Greenfield&rft.aufirst=Derek&rft.au=et+al+&rft.aulast=et+al&rft.aufirst=&rfs_dat=ss.included=1&rfe_dat=bpr3.included=1;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="http://dx.doi.org/10.1371%2Fjournal.pbio.1000137">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&rft.date=2009&rfr_id=info%3Asid%2Fscienceseeker.org&rft.au=Greenfield+Derek&rft.aulast=Greenfield&rft.aufirst=Derek&rft.au=et+al+&rft.aulast=et+al&rft.aufirst=&rfs_dat=ss.included=1&rfe_dat=bpr3.included=1;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=”http://dx.doi.org/10.1371%2Fjournal.pbio.1000137″>10.1371/journal.pbio.1000137</a></span>

Micro! Polo!: Discovering the beneficial bacteria needed to clean our messes

Micro polo

Bacteria do not have taste buds or eyes. However, they have very fine-tuned senses that relay information about the status inside as well as in their environment. To compete and survive in virtually all environments on the planet, bacteria have evolved to sense and utilize many chemical compounds (most of which are still unknown) for energy and existence no matter how we as humans feel about these compounds. Even toxic compounds are easily metabolized by some bacteria. Whether it is hydrocarbons like petroleum or groundwater contaminated with dry cleaning chemicals, bacteria have evolved pathways to utilize these compounds.

Imagine restoring highly contaminated land for public use without expensive machinery or excessive human exposure. Current research within DOE is working towards this goal through bioremediation, utilizing bacteria with ability to render radioactive or otherwise hazardous material harmless. Even though most microbes presently performing this task are unknown, meta-sequencing projects are turning up a common set of genes (and proteins) necessary for this process.

Let’s briefly take a look at some of these toxic compounds.

TCE to DCE

Here we have (from left to right) perchloroethene, trichloroethene, and dichloroethene. PCE is a common chemical used in dry cleaning and easily contaminates groundwater. It’s removal is expensive and time-consuming, not to mention dangerous given its toxicity. However, a small number (so far) of bacteria can actually use these chemicals during metabolism when oxygen is absent from the environment (deep underground, for example). DCE is still considered a contaminant, so, how do we get rid of it? A group of bacteria discovered not long ago actually have the complete set of genes to breakdown perchloroethene to ethylene, Dehalococcoides. These bacteria have small genomes relative to the average bacterium but contain a set of genes that will render these contaminants essentially harmless.

vinyl chloride and ethylene

Vinyl chloride, the next step in PCE degradation can be further reduced to ethylene by an enzyme called vinyl chloride reductase (Vcr). To date, only Dehalococcoides are found to contain Vcr genes.

Next, I will talk about other common contaminants and the wonderful bacteria that can clean them up.

“Write what you know about” – Mark Twain

Good advice from a great communicator. From now on, the majority of posts will relate in some way to bacteria, especially microbial genomics. Most of the remainder of posts will be related to science communication and education.

Why bother spreading the love for the little creatures? I believe this quote from microbialgenomics.energy.gov sums it up:

By some estimates, microbes make up about 60% of the earth’s biomass, yet less than 1% of microbial species have been identified. Because most do not cause disease in humans, animals, or plants and are difficult to culture, they have received little attention. Identifying and harnessing their unique capabilities will offer us new solutions to longstanding challenges in environmental and waste cleanup, energy production and use, medicine, industrial processes, agriculture, and other areas. Scientists also are starting to appreciate the role played by microbes in global climate processes, and we can expect insights about both the biological underpinnings of climate change and the contributions of microbes to earth’s biosphere. Their capabilities soon will be added to the list of traditional commercial uses for microbes in the brewing, baking, dairy, and other industries.

There is so much we don’t know about microbes. However, we are beginning to understand their enormous adaptability. Whether it is 30,000 feet above the ground or two miles beneath it, bacteria can inevitably survive. I will now focus on getting the word out about the little guys who can’t speak for themselves.

Microbes can be used in soil cleanup
Microbes can be used in soil cleanup (Photo credit: Wikipedia)