Chronologically impaired: how to know what to make of the term "ancient algae"

Its now been a really really long time since I have written. This is mostly due to the time constraints of a researcher who is doing many things at once. I have been teaching which has been wonderful but time consuming, I have been writing papers which is necessary but all consuming, and I have been writing proposals, coordinating workshops, starting new projects...etc...

But every once in a while an article comes along to remind me why I started this blog in the first place: to explain what the heck some of these reporters and business types mean when they throw scientific words around with algae. Today I read an article that was so misleading (in my opinion) that I was compelled to write. This article in ScienceDaily is trying to sensationalize an idea, while mangling the concept. They are reporting on this article published this week in the Proceedings of the National Academies of Science.

When people talk about ancient algae, my ears perk up. My dissertation research was on how to use geological evidence (fossils and preserved organic molecules) to tell the early evolutionary history of algae. I also attacked this problem using genes and making phylogenetic trees . One of my motivations for my research is the way people over-simplify the geologic record and want to take small pieces of evidence and make big stories out of them. That makes things accessible to people who's mindes aren't really built to think in geologic time - think about what 10 years means in terms of your life, or 100 years or 1000 years and then try to wrap your head around 100,000,000 years (100 million years).

The PNAS article is describing the biosynthetic pathway of some interesting and unique lipids made by the green alga Botryococcus braunii. B. braunii has always been described as a good target for biofuel production because it produces more lipids than any other microalgae described and it produces the unique botryococcenes that would be an easy-to-use lipid source for making biofuel. The only problem with B. braunii (and this is well documented) is that it grows super slow and thus makes it a challenging strain to grow for industrial use. The description of the genes involved in the synthesis of botryococcenes takes us one step closer to being able to engineer this pathway into an organism that grows faster. In my opinion this is a good idea in the world of algae biofuel ideas. The PNAS article briefly cites some articles that have found evidence of Botryococcus braunii lipids in the geologic record, one dating back to around 500 million years ago. It was a requisite reference to what is known about this organism, and well placed in the introduction.

The article in ScienceDaily took this idea and thought it was cool enough to make a catchy headline out of. Yes B. braunii is old, but so is the whole green algae lineage. There is not any evidence that Botryococcus is any older than any of the other greens often considered as biofuel strains (such as the many "Chlorella" species). The phylogenetic tree shown above,and published here, demonstrates that. There are lots and lots of green algal trees published, this is just one that I have published that has all the Botryococcus strains/species on it. Each step along the tree can be considered in evolutionary time, and nodes closer to the leaves of the tree are more recent than nodes deeper in the tree. So, it is not incorrect to say that Botryococcus is ancient but it is incorrect to believe it is any more ancient than other similar groups of green algae. Just for context, the most ancient groups of green algae could date back 1.6 billion years according to some interpretations of fossils from that time. It is also true that geologic evidence suggest that it has contributed to preserved organic carbon on a number of occasions but it is a fresh water organisms and to that that most of the oil that runs the planet, which is marine sourced, came from Botryococcus would be an exaggeration.

Algae Biofuels and Genomics - Where do we stand?

This week, I'm in California for the Joint Genome Institute's (JGI) Annual User's Meeting. The theme of this year is "Genomics of Energy & Environment", and there are a lot of talks in the next few days aimed at how people are using genome sequencing and bioinformatics for biofuels research.

In the algae world, we know some groups such as Saphire Energy are working to genetically engineer algal strains. People have also been working for years to try to engineer more hydrogen production from green algae, and we just learned of a group successfully genetically engineer algae to make proteins for the pharmaceutical industry.

In order to understand how to genetically engineer an organism, we need to have model genetic and genomic systems to learn from and experiment with. For a long time, very few things considered algae had a genome sequence. You hear a lot about the green algae Chlamydomonas reinhardii, because it was the first to have it's genome sequenced. In the past 10 years, only a handful of microbes that fall into the category algae have had a whole genome sequenced, including two diatoms and one of their relatives, a red alga, a coccolithophore, and two other marine green alage. Compare that to at least twice as many plant genomes and over one thousand bacterial genomes.

In my academic work, I use genomes and comparative genomics to study the evolution of algal groups and their physiological capabilities. I also use a new tool, called metagenomics, to look at the combined genome of these organisms in the environment - specifically the ocean. To do this, we go collect community samples of microbes in the ocean, extract total DNA (or RNA) from those samples and then sequence as much as we can from it. Then we identify who was there by comparing to the genomes we have already sequenced. As you might guess, this is a really hard problem when you have only a handful of genomes to compare to.

This limited genomic data also poses challenges for the algae biofuels industry. Many of the scientist doing this work would love to have genome sequence of the potential fuel producing strains. Two weeks ago, a group in Texas announced the genome project of a biofuel favorite, Botryococcus braunii.

http://www.sciencedaily.com/releases/2010/03/100312164659.htm

This will be a contribution to the industry but also to academia, where scientist looking to understand the evolution and physiology of these organism will also be able to make use of the data. B. braunii is just the beginning of sequencing for energy related organisms, that will also help to fill out our understanding of the tree of life.

(I should say that the genomes I mentioned above are the ones that are publicly available. Many labs are in the process of sequencing genomes that are not publicly available yet, and genome sequencing done through industry probably will not be shared... but we can hope.)