Blogging for Bacteriophages is proud to give you it's first guest post. This article comes from M. McGuirk., a biochemistry student at Chatham University.
Green algae are photosynthetic microorganisms capable of using protons as a reductant and producing molecular hydrogen. As technology advances, these organisms might provide an efficient, cost-effective method to mass produce hydrogen gas to be used as a renewable source of energy. Currently, hydrogen fuel is extracted from natural gas and other non-renewable energy sources, which release particulate matter and greenhouse gases into the atmosphere during their extraction and processing. Algal biosynthesis of hydrogen is particularly promising because it uses two of Earth’s most abundant resources, light and water, to form an "eco-friendly" biofuel.
Hydrogen gas production by green algae is a consequence of anaerobiosis, which forces the cell to rely on molecular hydrogen as a reductant. Green algae are exposed to anaerobic conditions in lake and sea sediments, which can become anoxic with insufficient water turbulence or excessive algal blooms. Historically, hydrogen production by green algae was induced by anaerobic incubation in the dark, which stimulates the expression of a hydrogenase enzyme.
The major roadblock for commercial application of hydrogen biosynthesis by algae is the fact that algal hydrogenases are inhibited by molecular oxygen. This sensitivity to oxygen has motivated extensive work to genetically engineer mutants of Chlamydomonas reinhardtii with more oxygen tolerant hydrogenases. The successful engineering of a more oxygen tolerant hydrogenase would put us one step closer to commercial biosynthesis of molecular hydrogen for fuel. Another approach to the problem of hydrogenase oxygen sensitivity is temporal separation of the water splitting and hydrogen evolving reactions.
Researchers have also shown that sulfur deprivation improves hydrogen yield by inhibiting molecular oxygen evolution. In the absence of necessary nutrients, metabolism and growth slow significantly too conserve the remaining substrates. In the case of green algae and other photosynthetic organisms, sulfur depleted environments stimulate the downregulation of photosytem-II and consequently, molecular oxygen evolution. Under these circumstances, electrons are not suf
ficiently removed by molecular oxygen. Green algae significantly increase hydrogen production under sulfur-deprived conditions because hydrogenase is charged to remove the excess electrons.
Hydrogen fuel offers an efficient, environmentally friendly alternative to gasoline and biodiesel. Hydrogen is a potent, cost-effective fuel because it has the highest energy content per unit of weight of any known fuel. Hydrogen gas production by green algae shows enormous promise, but requires a few manipulations to make the process feasible on a commercial scale. To improve this process, the number of hydrogenase expressed in the cell must be increased (without being toxic) to increase the yield of hydrogen per algal cell. The oxygen sensitivity of the hydrogenase enzyme must also be reduced so that the enzyme can produce hydrogen more efficiently in easily managed environments. It is highly likley that within our lifetimes, we will see algal hydrogen production on a commercial scale.
Friday, May 30, 2008
Free Hydrogen--Algal Biofuel Production
Monday, May 26, 2008
Winogradsky Column (Day 1)
I have decided that my microbiology education would be incomplete without experiencing first hand the creation of a Windogradsky Column.
This column was started yesterday with mud/silt from Panther Hollow "Lake,"and no extra nutrients or minerals were added. It's currently sitting in my living room window.
Friday, May 9, 2008
Mosaicism: The World of Horizontal Gene Transfer (Part 1)
Commonly, gene transfer is thought of as a vertical line from parent to offspring, along which all evolutionary traits are passed. However, as we began delving into genomic sequences, we found that this may not be true and that the lines between "species," especially on the microbial level, are quite fuzzy.
Horizontal gene transfer is the transfer of genetic elements between species. The microbial world is filled with examples of this phenomenon. This article is the first in a 3 part series that will explore the ever fluctuating genetic world of our microbial majority.
Escherichia coli is perhaps the most well studied and utilized bacterial organism on the planet. This bug also has the capability for a wide range of illness in humans including: non-pathogenic, enterohemorrhagic (such as popular strain 0157:H7), enterotoxigenic, and uropathogenic. The question is obviously raised--how can the same organism have such pathotypes, and what allows it to be versatile enough to thrive in such different environments as the urinary tract vs. the intestinal tract.
An article coming out of the University of Wisconsin-Madison shows that E. coli consists of a general common backbone that is nearly 100% identical across strains, yet only takes up 75%of the genome. However, they 
show that within this backbone are regions (islands) that are highly divergent between strains (See figure at left). It is no surprise that within these divergent regions contain the genes which allow for survival in different environments (pathogenicity islands)
These islands are distinct from each other, the surrounding genome, and the corresponding areas in other strains. However, the striking similarity between islands of different strains is that they all seem to be located in nearly the same locations.
Furthermore, strains of the same pathotype tend to have the same/similar genes located in islands (see figure below)--but not necessarily in the exact location or orientation. These islands tend to occur in areas at tRNA regions--commonly utilized by bacteriophages for integration.
Phages are clearly agents of horizontal gene transfer, further examination of these island regions show the presence of cryptic (non-viable) prophages. This indicates that at least 5 phages integrated, but subsequently lost genes required for the creation of viral progeny. It is possible that the other islands are also prophages, but gene loss has occurred to the point where they are no longer recognizable.What this means as a whole to the definition of species is to me, yet, unclear. Strains of E. coli all share a distinct backbone of metabolic genes, but differ drastically in their specialized regions. How do we decide which belongs in a species?...especially when we differentiate humans from chimpanzees (only ~6% genetic differences).
Welch, R.A. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences, 99(26), 17020-17024. DOI: 10.1073/pnas.252529799
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Saturday, April 26, 2008
Where the Wild Microbes Are: A New Theory on How Pathogens Survive Food Processing
Produce borne diseases have recently been gracing the front pages of our media. Our spinach has E. coli, our onions have Hepatitis A virus and E. coli, our strawberries have Listeria, and our tomatoes and peanut butter have Salmonella. Not to mention the countless tons of ground beef tainted with pathogenic E. coli.
Common sense says that washing and proper handling of our food should simply be enough to prevent illness outbreaks. It has now been hypothesized that many bacteria were able to "hide" within and among the plant cells, protected by their sturdy cell wall. Or even that some pathogenic bacteria were able to enter the cells and remain protected from traditional washing methods.
An article in this month's Applied and Environmental Microbiology looks at a much different method of bacterial survival on produce. They hypothesize that these bacteria are taking refuge in various protozoa, and 
subsequently are protected from washing and other sanitation methods due to being held either within the cell or an exogenous cell-derived vesicle.
The authors used protozoal isolates from store-bought spinach and romaine lettuce. They measured the concentrations of various microbes from the surface, and cultured a set of naturally occurring protists from these samples.
They show that not only are certain pathogenic bacteria (like E. coli 0157:H7) able to be taken up by protozoa, but that in many cases, they survive to be ejected into the world around, surrounded by a vesicle. The flourescent image at above shows this event happening with E. coli 0157:H7 and a strain of Tetrahymena.
Previous studies have shown that the bacteria in these extracellular vesicles are able to survive for the long-term, even in harsh conditions.
This paper shows us that microbial ecology is much more complex than we perceive, and that simple and obvious solutions may not always be the best. We now know that wild protozoa living on our produce can sequester pathogenic bacteria, and furthermore wet produce allows vesicles to be created containing viable bacteria.
Gourabathini, P., Brandl, M.T., Redding, K.S., Gunderson, J.H., Berk, S.G. (2008). Interactions between Food-Borne Pathogens and Protozoa Isolated from Lettuce and Spinach. Applied and Environmental Microbiology, 74(8), 2518-2525. DOI: 10.1128/AEM.02709-07
Thursday, April 10, 2008
Wild Bacteria That Eat Our Antibiotics? Of Course!
Antibiotics were invented by bacteria and fungi during thier conception in this universe. Used to control microbial niche environments, it wasn't until 1928 that Fleming (and subsequently Florey and Chain) began the widespread use of the antibiotic penicillin to control bacterial infections in humans. And so, the antibiotic revolution began.
Subsequent use (and misuse) of antibiotics has given rise to various resistant strains. These are becoming a vast problem in the treatment of diseases that once were "easily" curable, including the well-publisized MRSA and XDR-TB, as well as many others.
This paper, coming out of Harvard University, describes the isolation of bacterial strains that can live on antibiotics as their sole carbon source. Current thought states that resistance in a bacterial population occurs because of exposure in clinical settings (or a popular theme of dumping antibiotics down the drain). However, the authors show that even secluded environmental isolates have the ability to subsist on both natural and synthetic antibiotics.
Our antibiotics are just variations on themes we have seen in nature, and because of this, the environment represents a vast source of antibiotic resistance mechanisms that we have yet to discover. In niches exposed to antibiotics (ie. clinical pathogens) complete resistance is preferential. However, antibiotic metabolism (as described in this paper) would confer an advantage, even if it is only small in comparison.
I find it fascinating that in 11 different soils (urban, farm, and pristine), bacteria were present that could thrive on 18 different antibiotics as carbon sources! These bugs were not just living with the antibiotics, but were actually eating them!
We have much more to discover about antibiotic resistance mechanisms, this study clearly shows a direction that we can head to begin this task. Just as we looked to nature to develop antibioitcs, so must we look to nature to study how resistance works.
Dantas, G., Sommer, M.O., Oluwasegun, R.D., Church, G.M. (2008). Bacteria Subsisting on Antibiotics. Science, 320(5872), 100-103. DOI: 10.1126/science.1155157
Further Readings
Timebomb : The Global Epidemic of Multi-Drug Resistant Tuberculosis
Good Germs, Bad Germs: Health and Survival in a Bacterial World
Teaming with Microbes: A Gardener's Guide to the Soil Food Web
