MyTH: Week 7 focus: Pseudomonas fluorescens

Swimming bacteria
Swimming bacteria

My Tiny Highlight (MyTH) has been on hiedas for a while. However, I’m glad to introduce this week’s organism, Pseudomonas fluorescens. This will be the second highlight featuring a Pseudomonad (Week 5). For short hand, I will write the name Pfu. This is an interesting organism due to its effects on plants and other soil organisms. Pfu is a major constituent of the rhizosphere of plants. The rhizosphere is an active zone surrounding plant roots where soil microbes interact with the roots and each other usually in a symbiotic relationship. This is certainly the case for Pfu due to the benefits this microbe bestows upon host plants. First, Pfu produces many secondary metabolites that are probiotic for plants and can control bacterial and fungal plant pathogens. A major class of secondary metabolites produced are derivatives of phenol that display antifungal properties including 2,4-Diacetylphloroglucinolphloroglucinol, and phloroglucinol carboxylic acid. Secondly, Pfu also produces a type of antibiotics from phenazine that can be beneficial to both plant and microbe. Third, Pfu produces siderophores than can scavenge essential iron from the environment with very high affinity giving Pfu an advantage against other soil inhabitants that are less efficient at acquiring elemental iron. Siderophores are produced within the cell and excreted into the surrounding environment. Pfu contains outer membrane receptors that can transport iron-containing siderophores back into the cell. One specific siderophore, pyoverdin, has green fluorescent properties which give P. fluorescens its name.

Image of pyoverdin, also known as fluorescein.
Image of pyoverdin, also known as fluorescein.

In a later post, I will detail more about the rhizosphere and soil in general.

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 5 focus is Pseudomonas aeruginosa

Time again for My Tiny Highlight (MyTH) of a particular bacterium. This week is the infamous Pseudomonas aeruginosa. This trooper can be found almost anywhere on earth due to its ability to use all kinds of material as food including diesel and jet fuel. Most of us know it as a common infection you get while in the hospital because it is so darn hard to kill. If you know someone that suffers from cystic fibrosis, this bacterium can be fatal as it is commonly found in the lungs of these patients causing pneumonia. I personally learned about this bacterium in school when talking about hot tubs due to its resistance to disinfectants.

P. aeruginosa is one of the most famous microbes for forming biofilms. A biofilm is a group of cells that attach to each other and to some surface usually by secretion of sticky sugars from the cells. A common sticky sugar, or exopolysaccharide (EPS), excreted by P. aeruginosa is alginate, an uncommon sugar for bacteria since it is most commonly found associated with brown algae. Its existence in Pseudomonas has led to significant knowledge about the synthesis of alginate (alginate biosynthesis; another ring in the bacterial circus). This knowledge is leading to novel medical applications for alginate.

P. aeruginosa is also known for its role in a multicellular behavior which seems strange for a single-celled organism but is becoming more and more common. Quorum sensing was first described over 40 years ago. I beg you to check out Bonnie Bassler‘s TED talk about this. QS is how single cell bacteria are able to send signals into the environment to communicate with members of their own species and with other types of bacteria as a way to assess their population.

Another feature of P. aeruginosa is their modes of transportation, i.e. motility. P. aeruginosa has two major modes of getting around their environment, swimming motility with flagella or “twitching motility” on a surface using Type IV pili. We have discussed flagellar motility before (Chemotaxis). Type IV pili (TFP) is different. Pili are somewhat similar to flagella because they protrude out of the cell and are used to move around. Unlike flagella, pili don’t rotate but rather extend out before retracting back to the cell pulling the cell in the direction of the pili tip. The coordination of pili extension and retraction is guided by a chemotaxis-like pathway. Many bacteria have evolved to use chemotaxis proteins that have adapted to new roles within the cell.

I will end this MyTH with a special shout out to one of my favorite researchers, Carrie Harwood. Caroline Harwood is a professor at the University of Washington in Seattle. Carrie’s daughter suffers from cystic fibrosis and this led to Carrie’s curiosity in P. aeruginosa. She is a pioneer and a role model for many female scientists including Becky Parales. For her tireless career, Carrie was inducted into the National Academy of Science a few years back. A recognition well deserved.

Pseudomonas aeruginosa scientist Carrie Harwood. One of the nicest people in Science!
Pseudomonas aeruginosa scientist Carrie Harwood. One of the nicest people in Science!

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 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!

caulo

 

 

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!

 

MyTH: A new weekly series about one bacterial species. First Post: Escherichia coli

This thought came to my head as I couldn’t sleep last night. My Tiny Highlight (MyTH) will be weekly and will showcase interesting or useful bacteria. For the first installment, I will focus on the gold standard of biology; Escherichia coli or E. coli. E. coli was discovered in 1885 by a German doctor in feces of healthy people. He called it Bacterium coli commune because it was found in the colon. The classification system of bacteria was much different before the ability to sequence DNA as novel bacteria were initially classified and named by their shape and motility. The name later changed to Bacillus coli before finally being reclassified and named Escherichia coli after the original discoverer. How would you like it if someone named a bacteria from feces after you?

E. coli receives a bad reputation thanks to pathogenic strains that force recalls of all kinds of food products. However, those strains are very uncommon as E. coli is one of the most abundant species found in the GI tract of mammals. Also, without this bacterium, many of the scientific discoveries of the past 50 years would not be possible including solving protein 3D structures, mass production of insulin, and understanding signal transduction; the process of a cell sensing surrounding signals or cues and responding to them in a way that is favorable for the cell. One reason E. coli was such a well suited model organism is the doubling time or time to divide one cell into two daughter cells. A doubling time of only 20 minutes means in less than 48 hours, the mass of E. coli cells would roughly be equal the the mass of Earth and have the combined volume equalling a 1 meter thick layer of bacteria covering the entire surface of Earth (including oceans). This is incredible and gives E. coli a major advantage over slower growing bacteria.

I want to discuss, briefly, a major influence of mine. Julius Adler was born in Germany and became a lover of Nature as a child. He was fascinated with butterflies. adler

His lifelong passion has been behavior of living things. Luckily, he spent most of his professional career studying chemotaxis in E. coli although he now studies fruit flies. Adler is known as the father of chemotaxis, or the movement of a cell in response to sensing chemical signals. His landmark early papers in the journal Nature about chemotaxis in E. coli in 1966 and his later paper on the chemoreceptors, the proteins that interact with the surrounding chemicals, in E. coli laid the foundation that maid the chemotaxis system of E. coli the best characterized signaling pathway in Biology. In regards to chemotaxis, however, E. coli is on the simplistic side of the scale. For example, E. coli has 5 chemoreceptors and 1 chemotaxis operon, or a stretch of genes that are transcribed into RNA together but lead to distinctly different proteins that usually interact with each other. Through the explosion of genome sequencing, scientists can scan newly sequenced bacteria genomes for chemotaxis genes. The average number of chemoreceptor genes is roughly 5 times more than E. coli (~25) and it is more common for bacteria to harbor multiple chemotaxis operons suggesting most bacteria have evolved to use chemotaxis for regulate more than the motility behavior in these cells.

Let’s think a minute about why E. coli is ‘stupid’ compared to other bacteria. By ‘stupid’ I mean, they have less capacity to integrate signals from their surroundings into a cell response. Why doesn’t E. coli have 25 chemoreceptors, for example? For the answer, we just need look at where this microbe is found. The GI tract of mammals is fairly constant meaning there is less need to scavenge for a new home or adjust to changes in temperature or nutrients. We as mammals have no problems eating meaning E. coli has no problem eating as well. How about the other sequenced bacteria? They predominantly live in more variable environments like soil or oceans where is would be to their advantage to be able to sense a lot of chemicals or nutrients in their surroundings. Therefore, through evolution, they have acquired new abilities to sense through duplicating genes and mutating DNA favorably. Changing only a few nucleotide bases (A,C,G,T) could mean acquiring the ability to physically interact with different environmental chemicals that could serve as an energy source. Nature is awesome and she knows how to keep us, as observers, guessing.

You may feel I am biased about chemotaxis ( I am). This was my dissertation work in another bacterium. Check back next week when I will highlight a little known (publicly) soil bacterium, Azospirillum brasilense. If you have any comments, questions, or suggestions PLEASE LET ME KNOW!

 

Recommended reading about Julius Adler.