Illustration of a bacterium that poops electricity and can save the world: Geobacter Hi-Res

Geobacter, nanowire, bacteria, bacteria art, science art

MyTH: Week 6 focus: Anaeromyxobacter spp.

This week I will write about bacteria that I dare say any of my readers know about, Anaeromyxobacter. Time again for My Tiny Highlight (MyTH). These bacteria were only recently discovered, first in Michigan but later in other sites. They are a peculiar member of a familiar group of bacteria, Myxococcus. Unlike the name suggests, Anaeromyxobacter can grow in the presence of oxygen, but they prefer anaerobic environments. They are found deep in the subsurface and can metabolize hazardous material for energy production similar to other deltaproteobacteria like Geobacter. Compounds in the environment that contain chlorine atoms are usually not a good thing. Luckily, Anaeromyxobacter can utilize these compounds to produce energy. Needless to say, Anaeromyxobacter are very versatile metabolically speaking since they can respire on 2-chlorophenol (or other halophenols), Uranium, iron, manganese, oxygen, nitrite, nitrate, nitrous oxide, and fumarate, to name a few. As far as metabolism goes, these bacteria are about as robust as they come. I personally have studied the genomes available for this genera of bacteria for a postdoc proposal. I can tell you, these guys are remarkable on many fronts.

First, Anaeromyxobacter have over half as many c-type cytochromes as the model Shewanella, 69 to 40. Cytochromes are the workhorses of metabolism that guide electrons towards the final electron acceptor like oxygen, iron, or uranium. Cytochromes accomplish this by shuttling electrons on heme groups. It is not uncommon for cytochromes to have multiple heme groups. Remarkably, Anaeromyxobacter has one cytochrome that has an astounding 40 heme groups. Shewanella cytochromes have  up to 10 hemes, to my knowledge.

What caught my eye was the number of PilZ domain proteins encoded within Anaeromyxobacter genomes. Four Anaeromyxobacter genomes have been sequenced: A. dehalogenans 2CP-C, 2CP-1, and FW105-9 as well as Anaeromyxobacter spp. K. Peeking into the genomes, all four are dead last in the number of enzymes that breakdown the bacterial second messenger molecule cyclic-di-GMP out of 1822 genomes that have at least 1 (they have 1 each). All four genomes are middle of the pack for the number of genes encoding enzymes to synthesis c-di-GMP with 10 (rank 989 out of 2032). Are you ready for this? Two of the four genomes contain 21 PilZ domain proteins (the binding domain of c-di-GMP). This is fourth among 1321 genomes which contain at least 1  PilZ protein; fourth most! The other two genomes are not that shabby at 18 and 13 PilZs each (rank 14 and 22 out of 1321 genomes, respectively).  Take a look at Table 1 to compare these numbers to the genomes of two model subsurface organisms from Geobacter and Shewanella.

Table 1: Annotated enzymes and receptor proteins for the bacterial second messenger cyclic-di-GMP in representative dissimilatory iron-reducing bacteria.

 Bacteria                                 DGCs                   PDEs                          PilZs

A. dehalogenans                     

2CP-C                          10 (989/2032)*    1 (1822/1822)             18 (14/1321)

2CP-1                          10 (989/2032)      1 (1822/1822)             21 (4/1321)

Fw105-9                     10 (989/2032)      1 (1822/1822)             13 (22/1321)

Anaeromyxobacter

K                                10 (989/2032)      1 (1822/1822)             21 (4/1321)

 G. lovleyi             43 (105/2032)      17 (1240/1822)            9 (53/1321)

S. oneidensis      51 (53/2032)         30 (43/1822)            4 (959/1321)

  • indicates (genome rank/ total number of genomes containing at least one representative of the domain)

Based on annotations from MiST2 and Pfam proteome databases (http://mistdb.com/ and http://pfam.sanger.ac.uk/proteome/browse)

To me, this signifies that Anaeromyxobacter really rely heavily on sensing c-di-GMP to regulate their metabolism and lifestyle. This is especially true when you consider where in the genome the PilZ genes are found. For example, A. dehalogenans 2CP-C encodes 18 PilZ proteins. Several of the genes for these are in gene neighborhoods with nitrogen metabolism genes suggesting a genetic link between c-di-GMP sensing and nitrogen metabolism. I wish I could have studied these links between c-di-GMP signaling and metabolism in some capacity other than bioinformatically. However, those discoveries will have to go to the next chump in higher education.

animated cyclic-di-GMP gif, second messenger gif
110 different confirmations of cyclic-di-GMP

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 via 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).

 

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!