MyTH: Week 4 bacteria highlight: Geobacter spp.

Welcome to Week 4 of My Tiny Highlight (MyTH) series. This week I will focus on not a species. Instead, I will focus on a genera; Geobacter. Like the previous highlights, Geobacter are proteobacteria that has become relevant only more recently. Geobacter were first discovered and isolated in the late 1980s by UMass professor Derek Lovley. In a short amount of time, Geobacter has become a model organism in highly active research areas. These include bioremediation and microbial fuel cells. Several different Geobacter spp. are routinely found in soil and sediment samples from contaminated sites. For many bacteria, oxygen is not required to survive. During the course of evolution, many bacteria, including Geobacter, can undergo anaerobic respiration, or create energy without the need for oxygen. The first Geobacter genome was published in 2003 to much fanfare in the journal Science. One reason for this was the discovery that Geobacter are motile, having several chemotaxis proteins. Also found was an unprecedented number of cytochrome (111!) genes which are usually used for electron transfer┬ávia attached heme groups to the protein. The number of bound hemes vary between 1 and 27. Very impressive. In order to survive, these bacteria can use a host of molecules as an “electron sink” so their metabolism can continue. Geobacter have two main strategies for this; if the “sink” is soluble, they can utilize a host of cytochrome c proteins on their outer membrane exposed to their environment. If these “sinks” are insoluble like metals for example, they can essentially extend appendages from their membrane to the “sink”.

This is where it gets interesting…

These appendages called pili have extracellular cytochrome c proteins along their length. So, electrons are transported from inside the cell through the pili and cytochromes to the available electron sink. Essentially, they are able to conduct electricity as a means of respiration. Here are two animations showing the differences:

 

extracellular electron transfer, geobacter
Electrons: yellow
iron: black
MacA protein: dark green
PpcA: blue
OmcB: black
other outer membrane cytochromes: orange and light green
bacterial nanowire, bacteria, chemotaxis, microbiology, geobacter
A bacterial nanowire. Electrons (yellow) are passed through pili (purple) to OmcS (cyan) for reduction of iron (black).

 

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.