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Professor at University of California, Santa Cruz
Study Summary: Discovery of Mysterious Microbe Offers New Insights into Ocean Ecosystem. An unusual microorganism discovered in the open ocean may force scientists to rethink their understanding of how carbon and nitrogen cycle through ocean ecosystems. A team of researchers at the University of California, Santa Cruz characterized a novel species of cyanobacteria by sequencing the metagenome of an ocean sample with the new GS FLX Titanium series reagents. The study, published in Science, details the discovery of what the researchers believe to be a new form of cyanobacteria, a group of photosynthetic bacteria formerly known as blue-green algae. Unlike all other known free-living cyanobacteria, this species lacks the genes needed for carbon fixation and photosynthesis, the light energy-dependent process which converts carbon dioxide and water into sugars, and whose byproduct is oxygen. Importantly, the mysterious microbe is a specialist in another essential ecological function: It provides natural fertilizer to the oceans by "fixing" nitrogen from the atmosphere into a form usable by other organisms. The study is the first published " paper enabled by the new GS FLX Titanium series reagents.
What was the role of 454 Sequencing in the nitrogen-fixing cyanobacteria study?
Over 10 years ago I started looking for nitrogen-fixing organisms in the ocean. Nitrogen-fixation is a critical element of the ocean fertilization process and for controlling how fast microorganisms can grow. We thought that there must be some missing microorganisms out there that were fixing nitrogen faster than we thought. We began looking for nitrogen-fixing organisms using a genetic approach based on a gene sequence. Initially, we found sequences for nitrogenase genes that we could not account for by any known organisms in the open ocean. For many years it remained an elusive organism. We tried continuously and unsuccessfully to bring it into pure culture. We were stuck.
454 Sequencing was the only way to uncover the biochemical capabilities of this organism. What we found was a very unusual cyanobacteria. We never would have been able to culture it without sequencing data because it doesn't have the biochemical capabilities for photosynthesis that we expected. While we knew it was a cyanobacteria, previous research suggested that it expressed nitrogenase during the day. Nitrogen fixation is totally inactivated by oxygen, and most phototrophs fix nitrogen during the night and oxygen during the day or perform both in two different cell types. We also knew this was a unicellular organism, so multiple cell types was not the answer. What we found from the data was that it simply doesn't have genes for carbon fixation and photosystem II.
What was your experience using 454 Sequencing data to generate your results?
It was much more straightforward than we might have thought. The longer reads definitely made things easier because it allowed us to identify proteins with much greater confidence. The amazing thing is that we went from data to paper and print in the shortest time in my career. It really was because the data was so easy to interpret and the signal was so clear. It was pretty amazing.
What have been the implications of this discovery in your field of research?
There are a couple of long-term implications of the results of this study. For one, most nitrogen-fixing organisms also fix carbon and bring nitrogen and carbon into the oceans. People are interested in nitrogen fixers because they are trying to figure out how to get ocean biology to take up carbon dioxide out of the atmosphere and remove it to the deep ocean. These new cyanobacteria are going to play a very different role in that process than we thought. They are fertilizing and stimulating carbon fixation in other organisms, but they aren't stoichiometrically bringing in carbon like other nitrogen-fixers. Where the nitrogen-fixation is being performed by these organisms is going to change the ability of the oceans to remove carbon dioxide.
Another interesting implication is that researchers have been trying to get nitrogen-fixation in association with higher plants for decades. This new cyanobacteria serves as a model organism for a different way of carrying out nitrogen-fixation in the absence of photosynthesis. It provides an interesting model for a new kind of biochemical mechanism and may have implications in biotechnology. Finally, the finding also has evolutionary implications. We can argue about whether it lost or gained the genes but clearly something has happened. The finding may provide new insights into the evolution of prokaryotes.
What's your next step? How do you plan to use 454 Sequencing in the future?
We are chomping at the bit for the next step in this study, which is further 454 Sequencing of different populations of this organism. We are already planning our next 454 run. While we know this population lacks the photosystem apparatus, we don't know for certain if populations around the globe have similar or different features. Perhaps we will find an organism that is an intermediate in the evolution of these genes or we will find species that have completely different genes. Studying the population biology of this unique organism is clearly one of our next interests.
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