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.

Its been a long time since I have written, its been a very busy few months. This spring (spring 2010) I taught a marine algal course for the University of Washington, which overlapped with my field work studying natural algal blooms that are part of a long term study I have started in Washington state (picture is taken while sampling water from depth with a niskin bottle). We have much to learn about algal community dynamics by observing natural blooms and field work is so much fun! This was followed by a trip to DC for a NSF panel on Sustainable Energy, and then a few months writing grant proposals and catching up with data analysis. This spring, the algal biofuels scene was pretty quiet so I didn't miss much, but lately there has been some news so stay posted for much commentary to come - from the gulf oil spill to genetically engineered algae.

Open Ponds vs Closed Reactors: some science behind how to grow lots of algae

Last week, Bodega algae was featured in an article in biomass magazine: http://www.biomassmagazine.com/article.jsp?article_id=3618

The article discusses the ongoing debate about open ponds vs closed photobioractors for growing algae on a large scale. Obviously, as part of a company working on photobioreactor technology, I am in favor of closed systems for industrial applications. I will go over some of the science here and say up front that I do see the advantages of open ponds - mostly their lower capitol costs than photobioreactors, but I think that with a little more research and development we will be able to engineer reactors that will not be prohibitively expensive.




1)Controlling growing conditions
The first thing to consider when thinking about cultivating microbes on a large scale is what are you growing. There is a lot of working being done on strain selection buy a number of government labs, academic labs, and private companies. They are all trying to determine which algae will grow best, under what conditions, and which will produce the most lipids. This is because not all algae are the same physiological and biochemically - not to mention their diverse evolutionary origins (see http://algaeenergy.blogspot.com/2010/03/what-are-algae.html ). At "normal" culture conditions algae do not grow that densely. Since the we are algae talking about grow photosynthetically in water, an algal culture is mostly water. A typical, run of the mill culture will yield roughly .1 g biomass/L. Now there is a huge range of growth rates in algae. Some are like weeds and will grow very fast, some are specialist and will grow really slow. The fastest growing ones, under normal condition can produce .5g biomass/L. The predictions to make growing algae as a biofuel feedstock economical is that we would have to grow at least 10 g/L but maybe even more like 50 g/L. Some people have achieved these densities in very specialized systems with small volumes on the order of 200 mL and I have heard claims that individuals or companies have achieved these densities in larger volumes recently but this is no simple task. Therefore, to produce very high density cultures in large volumes as the industry needs to, we need to do something clever. I often describe it as "factory farming" the algae. We need to engineer the algae or we need to engineer the system to be optimal growing conditions. Closed bioreactors allow for careful control of growing conditions where open ponds are subject to the weather. In the event that some group wants to grow genetically modified algae (I'll speak to this matter in another post) they would need to do this in a closed system so that the gentically modified organism was not allowed under any circumstances to be released to the environment.

2. Contamination
One of the biggest problems for the long term in any cultivation of algae is contamination - but this is especially problematic when growing on a large scale. In the lab, scientist take careful measures to make sure they are always working with sterile equipment, transfer algal culture in laminar flow hoods that limit the number of air born particles that come in contact with the culture, and they transfer the culture often to make sure an individual strain stays healthy. In large scale cultivation, it is difficult to control all these factors. In a open pond, it can be almost impossible. A friend mine who works on open pond systems said their group is focused on isolating natural strains that are already known to do well under local condition against competitors. This is true, and a cleaver strategy. However, we still do not understand all the aspects of the delicate balance found in microbial communities. Thus, I think it will always be difficult to control and maintain algal growth in open ponds where the culturing system is in contact with the open air. Close bioreactors are subject to contamination issues as well, but careful design and management can greatly reduce to chance of contamination.

3. Footprint
On of the benefits of using algae is their cultivation doesn't necessary require a large land footprint or arable land. Many of the open pond designs are large, shallow ponds that have a large surface area. Close bioreactors have flexibility in their design to allow for various shapes, stacking, integration with other building structures, and in general can have a much smaller footprint for the same amount of volume cultivated. In both cases, the biggest obstacle in scaling up is light limitation. In dense algal cultures, the optical path, or the distance light can travel through a material, is 3 in. That is why some many of the photobioreactor designs are thin plates, tubes, or bags. This is also why open ponds must be shallow. So photobioreactors techologies, such as Bodega Algae's reactor, work to get around this limitation by delivering light into larger volumes. If this can be done efficiently and with inexpensive materials, its possible to start cultivating much larger volumes without light limitation. For high cultivation densities, the algae need to have just the right amount of light. Too much light causes photoinhibition, where the cellular activities are shut down, and too little light means that the system is not as productive as possible. Light can be much easier to control in a closed system which optimizes the amount of biomass per unit area.


As things stand now, photobioreactors are still much more expensive than open ponds systems. What I like about our work at Bodega Algae is we are working toward bringing the costs down by engineering smart reactors with limited moving parts and inexpensive materials. As the article in Biomass Magazine says, there may be room for both open ponds and closed systems in the ultimate algae cultivation solution.

Join the Conversation on the future of science... your ideas straight to the White House

I received an announcement the other day from AAAS, soliciting ideas from the scientific community that can help shape Obama's science policy and direction in the coming years. I love the idea. Its so often, as one scientist doing your own research that is just a small piece in a large puzzle, to feel like its hard to figure out how to move what you know into the public sphere. That is why this solicitation by the white house is so exciting, they want to hear from everyone who has a good idea, and perhaps a new perspective. Of course Obama has a team of heavy hitting scientists to advise him as well as the whole AAAS and the National Academy of Science.... but with his administration's very grass roots mentality, they want to hear from a broad scope of ideas.

see: http://promo.aaas.org/expertlabs/grandchallenges.html

I am submitting a few statements on using large scale sequencing projects to study communities of eukaryotic phytoplankton (aka "algae"). They are important for controlling the carbon cycle in the oceans and they have potential as a sustainable biofuels feedstock. I believe algae could be part of distributed generation energy systems that will provide sustainable energy production on local as well as regional community scales. One thing slowing down current progress (if not holding us back) is our limited basic science knowledge about these organisms. With new genomic (DNA sequencing) and transcriptomic (RNA sequencing) methods we are able to make quick progress in understanding the basic biology of these organisms. The progress we are now making in leaps and bounds is the result of next generation sequencing technology, which is high throughput (generating hundreds of thousands and even millions of sequences in a single run) and is cost effective enough to employ it large scale. As a scientific community, we are using these new technologies for a great number of studies, but we could still do more and be more strategic. How about a new and improved, well coordinated and well funded aquatic species program. The more we learn about algal physiology, the more we learn about the ocean's biological response to climate change as well as ways to improve algae as a biofuels feedstock. Seems like a win win situation for me.

Are the environmental impacts of producing algal biofuel greater than conventional crops?

There is a blog post today on Forbes online that summarizes a new paper in the journal of Environmental Science and Technology. (http://blogs.forbes.com/energysource/2010/04/07/report-says-algal-biofuels-may-not-cut-carbon-emissions-but-read-more-closely) This summary inspired me to read the original article, which suggests that the environmental impacts resulting from the production of algal biofuel are greater than that of traditional crops.

The article by Clarens, et al. from the University of Virginia (http://pubs.acs.org/doi/abs/10.1021/es902838n) says that if the nitrogen and phosphorous needed for growth need to be mined and carbon dioxide used to enhance growth is added from compressed gas transported to the site of the algae culturing, then the carbon dioxide emitted in the process is greater than that sequestered by the algae growth. Not surprising. The authors then say that if you grow algae on waste water (for the N and P) and with flue gas for the enhanced carbon dioxide for growth, then you can side step the negative carbon balance. If you read my other posts, you'll see I fully agree. We have to be recycling waste water and carbon dioxide if algae will ever be a part of a sustainable system.

The authors make assumptions for their model that include growing algae in raceways that are aerated with paddle wheels and fertilizers are used as flocculants. Harvesting is a combination of flocculation and centrifugation, which is an old idea and a very power hungry one. I like the idea of this kind of energy balance modeling, but it would be nice to see the results with a new and more innovative cultivation approach.

The success of Solazyme: what they are keeping in the dark

Solazyme, a San Francisco based algae biofuel company has received a lot of press and attention lately, including a large amount of funding and a mention in last week in the economist http://www.economist.com/business-finance/displaystory.cfm?story_id=15773820. As the economist says, Solazyme is an anomaly. Unlike other biofuels companies, they say they will be delivering large volumes of algae oils soon (20,000 L of algal based biofuel to the US Navy). This feels like progress for the algae industry and its nice to see that a company that is aiming to produce algae based fuel actually doing so . But when you look into the technology Solazyme is using to make this possible, you will see that they they are using algae in a different way. They are growing algae to make lipids but they are not harnessing the power of the sun and photosynthesis. They are growing algae in a dark fermentor - essentially using the algae to convert sugars to lipid. This may be a clever loophole in the system of making high energy fuel from lower energy biomass, but its difficult to imagine this system can be a sustainable.

The science behind what Solazyme is doing:
Solazyme is growing algae in the dark. This may seem counter-intuitive since most of us know algae as tiny photosynthetic organisms. Photosynthesis is one of the only things that links all the algal groups together - since they don't all share a common evolutionary history, only a common functionality. Typically these organism only get attention as phototrophs, but actually most of them are photoheterotrophs. This means that in the presence of light, these organisms will photosynthesize. In the dark, they can respire - using biosynthetic pathways similar to many other heterotrophic organisms. In general, "respiration" just refers to any metabolic process that produces carbon dioxide.

In algae, the dark respiratory processes appear to function in the light to some degree as well as in the dark, because the various carbon compounds needed for growth can be synthesized through different pathways. In the dark where oxygen is not present, the organisms will undergo fermentation and in the presence of oxygen, they will employ glycolysis for metabolism, just like you and me.

Why would an organism do both photosynthesis and respiration? Well, why wouldn't an organism do both if it could. Since we tend to be very animal centric when it comes to thinking about biology, we think its weird to be metabolically diverse since we are so metabolically constrained. We can only gain energy from cellular respiration. The organisms that have multiple modes of metabolism hedge their bets and can survive and even grow and reproduce under a range of conditions. It turns out that most algae grow just as well using external sugar as they do photosynthetically. Depending on the condition, algae can do a combination of these metabolisms.

Solazyme is growing their alage in fermentation reactors - presumably without oxygen and definitely in the dark. See the schematic below from their web site.


However, Solazyme's process is still dependent on photosynthesis, which is responsible for creating biomass that is then fed to the algae. They say their system can utilize any kind of biomass available to feed the alage, but they still need to convert it to sugar which can be one or more production steps. It is understandable why they took this route. They can consistently grow algae in high density, they don't need to worry about how to get light into a closed system, and they can use a tried an true reactor system. But how can it be sustainable?

Sustainability, economics, and energy mass balance:
It appears that Solazyme is collaborating with a BlueFire Energy, a next - generation sugar producer (http://www.greentechmedia.com/articles/read/from-hype-to-reality-not-all-algae-were-created-equally/ ) that can produce sugar from agricultural waste products, recycled paper, and other sources of biomass. If so, this seems like a reasonable source of sugar. Solazyme's dependance on this other system of producing sugar means that there are a lot of energy requiring steps involved. There is energy used to grow, harvest, or collect the initial biomass. There is energy used to move the biomass to the sugar production facility and then the sugar to the algae production facility in addition to the energy used in extracting the oil from the algae. It is hard to imagine all these energy inputs could equal the energy out. We know that biofuel made from conventional crops suffers from this problem. For the production of biofuel from any source to be a solution to diminishing energy resources, it needs to be as simple as possible

I feel that what really makes algae based biofuel a sustainable option (if not an economically viable one) is that it can remediate nutrients in waste water and can utilize carbon dioxide that would be emitted to the atmosphere. In this situation, we envision a closed loop. If the energy provided for photosynthesis comes from the sun, then there is very little energy in so that any energy out is a bonus to the benefits of remediation. In working toward sustainability, Solazymes fermentation reactors could be co-located with its sugar production to limit the energy in. Because all algae companies technologies are top secret, I can't claim to understand everything Solazyme is doing, but it is important to keep sustainability at the forefront of our technological development.

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.