Living at the Boiling Point: What we can learn from extreme heat-loving microbes

Thanks to the decreasing costs of sequencing genomic DNA, finding novel microorganisms that add to our understanding of metabolism in myriad environments is becoming common place. Not only are we learning about the diversity of life in extreme environments, like heat, cold, pressure, and altitude, but we are also learning what life on other planets may be like. With each additional genome added into ‘the cloud’, our synthetic biology toolbox gets a little bit bigger and our ability to manipulate tiny organisms to produce novel compounds is possible. Enter the “rushing fireball”.

Pyrococcus furiosus is an archeal species that thrives near deep-sea thermal vents where temperatures are between 90 and 100 degrees Celsius (or 194 to 212 degrees F). P. furiosus can grow at temperatures as low as 70 degrees C (158 deg F). To live in such conditions, this organism’s proteins must be tolerant to what we would consider harsh conditions. This organism’s ambient conditions makes wild-type proteins well-suited for industrial processes where temperatures are near boiling.

So far, P. furiosus has been utilized to produce 3-hydroxypropionic acid, a common industrial chemical used to make various products including acrylics. The kicker is that these cells were wired to make this chemical from atmospheric carbon dioxide. It is not crazy to think of what other useful products can be produced by P. furiosus with small modifications within the genome; products like ethanol or butanol as biofuels.

Pyrococcus furiosus, bacteria, archea, illustration, microbiology
My illustration of Pyrococcus furiosus

Reference

Keller, M., Schut, G. J., Lipscomb, G. L., Menon, A., Iwuchukwu, I., Leuko, T., Thorgersen, M. P., Nixon, W. J., Hawkins, A., Kelly, R. M. and Adams, M. W. W. (2013) “Exploiting microbial hyperthermophilicity to produce an industrial chemical using hydrogen and carbon dioxide”Proc. Natl. Acad. Sci. U.S.A. (in press).

Combing the Earth One Genome at a Time: In Pursuit of “The Next Big Thing” in Sustainability

animated bacteria, cellulose, bioenergy
Illustration of Clostridium thermocellum cells (orange) on the surface of a cellulose fibril (multicolor)

There is one thing that can be said about scientists: they’re never satisfied…thankfully. Observation and curiosity leave them on a never-ending quest to understand Mother Nature and improve humanity. One great example of this is the field of alternative energy science. Through the efforts of the Bioenergy Research Centers (BRCs) and Joint Genome Institute within the U.S. Department of Energy‘s Office of Science, there is a perpetual search for Nature’s best metabolic machinery. This search requires thinking outside the box and sometimes outside your comfort zone. For example, last year researchers from the Joint BioEnergy Institute published findings that originated in the El Yunque National Forest in Puerto Rico, a rain forest and home to Enterobacter lignolyticus, a bacterium that is tolerant to ionic liquids (liquids with salts that are not crystaline, but are liquid). This discovery began with the observation that soil microbes at El Yunque have a high rate of organic decomposition and tolerance to osmotic pressure.

Another example are bacteria from the genus Caldicellulosiruptor that are able to degrade biomass, however, they live in extremely thermophilic environments like hot springs from New Zealand to Russia to Yellowstone. Researchers at the BioEnergy Science Center were able to isolate these microbes and start characterizing the enzymes responsible for degrading woody biomass into simple sugars.

Or what about  researchers at the Great Lakes Bioenergy Research Center essentially dissecting a leaf-cutter ant colony in Panama to examine its ecology; from the fungus the ants use as food, to the bacteria that help degrade the leaves. Or what about isolating microbes from termite guts or wasp guts?

Then there is the champion for raising scientific curiosities, Clostridium thermocellum which holsters woody biomass degradation factories attached to the outside of its cell membrane. These factories are known as cellulosomes.

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>

Mimicking nature to convert sunlight to fuel #climatechange « Taking Science to the People

Mimicking nature to convert sunlight to fuel #climatechange « Taking Science to the People

This has been a dream for a long time. I worked as an undergrad on using spinach photosystem I to produce hydrogen using light. Biomimetics are huge and gains have been made on the photosynthesis front. One person to look at is Barry Bruce at the University of Tennessee. A few years back Forbes named Barry one of ten people that could change the world. I’ve known Barry for a long time and can say he is full of sh!t, but he is also full of great ideas and passion. His work with M.I.T. has helped revolutionize the efficiency of using direct sunlight as a fuel. Barry always uses great facts in his presentation about how much actual energy the earth receives from the sun and how little humans have been able to tap into it ( I think it’s around 1%). With more research, maybe someday we will be able to utilize 2%. (cross your fingers)