Our love hate relationship with algae

We often get mixed messages in the media about algae. I was thinking about this yesterday, while introducing my students to the role algae play in global biogeochemical cycles. Algae are the heroes of the planet I told them. This wisdom could be considered a euphemism for those that want to see the world from a plant centric view and are used to thinking about algae as stinky pond scum. I think the statement is quite accurate and was passed down from my graduate school adviser, who was sure it was one of the first things he told his students. So I told my students how things considered algae (see http://algaeenergy.blogspot.com/2010/03/what-are-algae.html ) are responsible for the oxygen in the atmosphere because oxygen is a biproduct photosynthesis. I also told them how micrscopic algae were mostly responsible for controlling the carbon cycle on the planet through a process called the biological pump.

This is a intricate cycle occurring in the oceans, where there is a balance between photosynthetic organisms (algae) producing biomass and oxygen from carbon dioxide and water, and heterotrophic organisms who eat the algae and breath off carbon dioxide. If this cycle was perfect, then carbon dioxide and oxygen would stay in steady state in the atmosphere through time, and the atmosphere would have never oxygenated, because each time oxygen was produced, it would have been consumed. Luckily, the biological pump is leaky pump, and some of the algae biomass that derived from carbon dioxide in the environment is "fixed" it into organic molecules that can sink out of the system and gets buried on the ocean floor. This buried organic carbon - when buried in high quantities - eventually becomes oil and natural gas over millions of years.

So this is a simplified description of a complicated process but it demonstrates that yes, algae are our heros! Thanks algae for the oxygen, and for sequestering carbon at a continual rate, and for sourcing the petroleum that makes our world run.

But then I talked to my students about dead zones. We learned how nutrient run off from rivers causes algal blooms. Nitrogen and phosphorous work to fertilize the plant on land - specifically the crop that produce affordable food - and they also work to fertilize algae once the excess reaches lakes and oceans. When the algae bloom as a result of the nutrient addition, they are quickly eaten by other things like protist, zooplankton and bacteria, that turn all that carbon that is now in the form on algae biomass back to carbon dioxide. In the process, the heterotrophs use up all the oxygen produced by the photosynthesis in the bloom and then some. Because the fresh water from the rivers floats on top of the sea water - called a lens - its hard for the oxygen in the atmosphere to penetrate the lens and the bottom waters remain oxygen poor. Thus a dead zone forms and animals that move leave, and animals that can't die. In this case algae get a bad rap. Algae also are put in the villain role when the group that blooms is a toxin producing bloom which seems to becoming more frequent.

So there you go, in one case algae are the heroes, on the other they are the villains. As I have watched the development of the algae biofuels industry in the past few years, it appears that this little critters play both parts in this sector. On one hand, people sing the praises of algae, preach about their potential as high lipid producers, remind us that they can grow on waste water and won't compete with food for arable land. This is all true. But then we hear frustration that none of the companies can produce high quantities of biomass and the cheep way to produce algae biomass in bulk doesn't work well(ponds) and the more expensive way (photobioreactors) is too expensive, and in general it is taking a long time to figure it out. This is true too, and thus algae have gotten a bad rap again. As I mentioned in a previous post, I think overcoming the challenges to using algae as a feedstock for energy production will just take a bit more time and patience than using something like corn or soybeans where we know just about what ever gene in their genome does under various physiological conditions or we will know soon (see a post about updates on genomics of energy grops from the JGI meeting (http://redgreenandblue.org/2010/03/30/the-genetics-of-fighting-climate-change-part-1/#more-3777). The state of algae genomics is just not in that place, but the academic community and industry are moving forward at a rapid pace. Just because they are small, doesn't mean that they are simple. Its rare to find a jack of all trades and a master of all too. Algae, are a sort of organismal jack of all trades, and they are already the master of a number of global processes.

Is engineering biology the future of energy?

Jay Keasling, the CEO DOE Joint BioEnergy Institute (JBEI) http://www.jbei.org/ and Professor of Chemistry Engineering and Bioengineering at UC Berkeley thinks so. I heard him give a keynote presentation at the DOE Joint Genome Institute's (JGI) annual meeting this week. Keasling gave a captivating talk about how to apply engineering principles to biology. He said that if you want to build a computer, you don't start from scratch. You make a design, buy the components that are manufactured by someone else, and then build your computer. He then made the same analogy to engineering a chemical plant. You decide what you want to manufacture, you design a factory, and then go buy parts for the factory - all of which will have standard fittings, connections, and sizes. He suggest that in theory, we should be able to engineer biology in the same way.

The biggest difference however, is that with computers and chemical factories, there is a knowledge base to build on. Biology does have a knowledge base of sorts, but not exactly. Most scientist conduct experiments in their own labs their own way, and often do not provide the data or knowledge to the public in any useful way in which to build on. Keasling suggested that we work to standardize and share. The day before his talk, I attended a workshop led by DOE and JGI about how to build a "knowledgebase" database for biology and how to standardize our data so that it can be shared. After the intro to Keasling's talk, it all started to make sense. I understood DOE's motivation for the knowledgebase- after all, the mission of the JGI is "to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup."

After sitting in a workshop all day hearing contradictory views on making standardization protocols (standardizations can stifle creativity), different ideas about work flows, varying estimates of data sizes, and differential needs of the community, I was a bit skeptical that we would see a functioning "knowledgebase" for the genoimics community any time soon. Its not that JGI or the scientists involved aren't doing a good job - I have put my ideas in the hat - but this is a really hard problem, made even harder by the system of funding and tenure in academia, which publishes most of the genomic data. Academic science is about competition for grant money, which doesn't always promote sharing and most labs find their own ways to do analyze data. In computer engineering, parts are standardized because that is the most efficient way to do it and everyone makes more money. For biology to be standardized to encourage efficient engineering, ideally there would be more money for research and the results would be open sourced. JGI and JBEI are part of the government and thus are trying to generate this type of open source data for the community.

Going on the really interesting things Kealing had to say about his group's success in engineering lipid biosynthesis pathway into E. coli, along with complementary gene pathways for breaking down cellulose into sugar to feed itself and exporters to export the newly synthesized lipids out of the cell for easy harvesting, I'd imagine that we will start to see some real progress in this area soon.

If you are interested in JGI's energy genomics program, see this new promotional video they made with ex'pression college for visual arts:
http://www.youtube.com/watch?v=qchN5FX_QN0

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.)

Algae making drugs?!

A recent article in the MIT Technology Review http://www.technologyreview.com/biomedicine/24826/page1/ discusses a new paper published in the Plant Biotechnology Journal http://www3.interscience.wiley.com/journal/123314076/abstract by Rasala et al. at UCSD.

The article in the Tech Review describes how the Rasala et al have been successful genetically engineering a photosynthetic green algae to produce proteins used in drug production. These proteins are currently produced by cultured bacterial and mammalian cells for harvesting by the pharmaceutical industry. The idea for inserting the genes for these proteins in algae is that over the long term, algae should be much easier and cheeper to grow than mammalian cells and algae can produce more complex proteins than bacteria, therefore a better option. Its an interesting idea....

what kind of world does biofuel fit into?

I was reading a recent article by Greg Lindsay for Fast Company (http://www.fastcompany.com/1583947/peak-oil-new-urbanism-biofuels-solazyme) in which he was challenging us to think about peak oil and energy in light of what he calls Jevon's Paradox. This idea was named after the 19th century Geologist who observed "peak coal", which prompted him to ask the question, "Are we wise in allowing the commerce of this country to rise beyond the point at which we can long maintain it?"


Lindsay goes on to wonder if next generation biofuels will just help encourage societal behavors that create an insatiable demand for energy, while avoiding the true issue that our species is living beyond our means on this planet. He points out that the choices we make now will shape the landscape of the planet in the future. Lindsay says, "Energy, transportation and urbanism are inextricably entwined, but as far as I can tell, no one has asked the founders of biofuel startups what kind of world they envision if they succeed."

Well, hot dang! I love it when I get asked questions like this... even if it was meant to be rhetorical. In the rest of the article, he interviews Jonathan Wolfson, the co-founder of Solazyme, a San Francisco based algae biomass producer. Jonathan gives nice answers and you should go read the article to see what he thinks.


The world I envision uses diverse energy sources and distributed generation. Renewables such as solar, wind, tidal turbines, hydro and micro hydro, and biofuel will all have their place. All of these energy technologies leave an imprint on the planet with some unsavory side effects such as disturbing animal migratory patterns or changing our aesthetic surroundings, but as long as we are going to continue to live in a technological world, we need energy. The really nice thing about algae based biofuel is the way it can easily fit into existing systems, provide a bridge to an economy less dependent on liquid fuel, and essentially do no harm (except cost money to build infrastructure and maintain).

But beyond just producing fuel, algae have a lot of positive attributes. Algae can recycle CO2 emissions - in any situation now or in the future where CO2 is being emitted, the gasses can be funneled to algae and they will happily grow. Algae can remediate waste from non-potable water. Algae don't require arable land, they have very flexible physiologies, and they are found everywhere, all over the world naturally. Growing algae is a win win situation, once we've figured out the technical issues involved in scaling up algal cultures that are dense enough to make high quantities of oil (or be economical in some other way). This has proven to be difficult but not impossible. Its only been a few years since there has been a big push to produce high quantities of algae biomass and the scientific knowledge behind algae was a far cry from that of other industrial crops like corn and soybeans which have been genetic model organisms for a long time. We hardly even know what some of the algal strains are that are being isolated and tested, much less have a genome for them. Just a few years ago, I was one of a very small group of graduate students attending academic algae meetings... we were a small crop of people working in a pretty marginal field.

So what I'm saying is give the industry some time, and algae fuel could buy us some time to transition the economy. In the mean time, we can clean up some water and air in the process.

Bodega Algae and Bigelow Labs in the news today - Portland Press Herald

Bigelow lab hoping tiny pays off big | The Portland Press Herald / Maine Sunday Telegram

Today, Bigelow Labs and their collaboration with Bodega Algae was featured in the Portland Press Herald (Portland, ME). It is a nice article highlighting the work Bodega Algae and Bigelow are doing to study the effects of lighting technology on the growth of a number of strains of algae. This effort is supported by a grant from the National Science Foundation SBIR program awarded to Bodega Algae to develop technology to reduce the cost of producing algal biomass. Willy Wilson from Bigelow Labs and his technician Sheri Floge are conducting detailed physiological studies at Bigelow while the Bodega folks in Boston are continuing with larger scale tests in the Bodega light enhanced bioreactor. The results of these tests are driving the development of a 250,000 L reactor. I'm excited to be working with Bigelow and anxiously awaiting more data to crunch in the next few months!

EPA to consider ocean acidification under clean water act.. and how it relates to algae

This week, the EPA agreed to consider ocean acidification as a water quality issue that can be addressed under the clean water act. This move by the EPA is part of a settlement of a lawsuit brought against the EPA by the Center for Biodiversity in Washington State. The Center for Biodiversity sued the EPA for not protecting coastlines against ocean acidification, which is a direct result of increasing CO2 in the atmosphere. This settlement means that the EPA will consider ways states can limit the CO2 pollution that is cause the acidification. What's so interesting about this problem is that the amount of CO2 already in the atmosphere is predicted by scientists to be great enough to cause the ocean pH to fall to levels dangerous to organisms that make shells. This means, even if we stop burning carbon tomorrow, there is still enough CO2 in the atmosphere NOW to cause a problem. This fact makes ocean acidification different than other climate change issues. It is not a prediction like how warm the surface ocean will be in 20 years or what percentage of CO2 in the atmosphere will be - it is a value that can be measured now.

So, the only way to prevent ocean acidification would be to take CO2 out of the present atmosphere. That is not an easy task. A lot of ideas have been proposed to engineer this CO2 removal, which is often called carbon sequestration. Some people suggest pumping it to the bottom of the ocean or liquefying it and pumping it deep into the ground. Other, more realistic solutions include removing CO2 by stimulating plant growth. This can be in the form of carbon credits for leaving preexisting forests or planting new forests. Other, popular proposed solutions involve growing algae. One option involves fertilization of the areas of the ocean were algae are not blooming due to nutrient limitation. Usually, these "deserts" in the ocean are limited by iron, and experiments where iron is added stimulates algal blooms. Now this does, in the short term, allow the algae to facilitate the removal of CO2 out of the atmosphere as they grow. However, it is unclear how long the CO2 stays out of the atmosphere, because other organisms eat the blooming algae or the sinking biomass after the algae die, sending that CO2 right back to the atmosphere - just like we exhale CO2 sequestered in plants like spinach after we eat them.

What may be one of the best solutions for carbon sequestration is controlled algae growth. This means growing lots of algae in bioreactors where we have control over the resulting biomass. Many of us in the algae biofuels industry are trying to do just this, in order to provide a feedstock for biofuel. If we "sequester" the CO2 this way, again, the CO2 will be returned to the atmosphere once it is burned as a fuel. If the CO2 to grow the algae didn't come from the atmosphere but from the smoke stacks of power plants that are emitting CO2 from burning coal or natural gas, the biofuel that results from this process is carbon neutral. This helps curb the future emissions of CO2, but won't help us remove CO2 that is currently in the atmosphere.

The only way then for carbon sequestration from algae to be a reality for reducing current CO2 levels, is for it to be more valuable for us as a society to produce a bunch of biomass for long term burial (on the order of millions of years) rather than for more fuel. Burying biomass is not currently economical and won't be until we place more value on reducing atmospheric CO2 than having fuel. This is where cap and trade comes in. Our government can decide pass legislation to cap the amount of emissions any one company can produce and then if they produce more than that, they can trade for other, more efficient companies allotted emissions, or buy off their extra emissions with carbon credits. This would require a lot of work by the government and a lot of cooperation on the part of industry...... and will be the topic of another post....




http://www.nytimes.com/aponline/2010/03/11/us/AP-US-EPA-Acid-Oceans.html?_r=1&scp=5&sq=EPA%20lawsuit&st=cse

What are Algae?

People are talking a lot about "algae". We can make biofuel from algae that are grown on waste water while remediating carbon dioxide - and we can do this without using precious farmland that is needed to grow food. "Algae" are the wonder critters. But what do people mean when they say "algae". As a scientist who works on these things (and loved them even before they were going to save the world), I wince at the broad use of a term like "algae" which is actually representing a huge group of organisms that can be much more different from each other than you are to a mushroom.

What unites things that are called algae is photosynthesis AND the fact that they are not land plants. Some algae - the green algae - gave rise to land plants about 400 million years ago, so they are all in the same family. But other algae, like diatoms, one of the most important photosynthesizers in the ocean, are not at all related to plants. The fact that diatoms do photosynthesis in a similar way to plants is a more a matter of history than of family. So why do these groups all get lumped together into one group that is ostensibly taxonomically useless? Well, that's historical too, resulting from the days when we saw the world as made of up plants, animals, and others. Now, with a century of experience behind us and armed with DNA technology, we now know how diverse the group of organisms called "algae" really is.