A crash of algae, bioterrorism and the future of biofuels

Photo by Jeff McMillan

What knowledge can we port from the shadowy world of bioterrorism and its countermeasures into the commercialization of algae biofuels?

Turns out, quite a bit — as a Sandia research team is demonstrating.

There’s a den of wolves, a troop of apes, a clutch of hens, a clowder of cats, a swarm of bees — even a murder of crows and an exaltation of larks. There isn’t an accepted collective name for algae we know of — but if there were, it would probably be a crash of algae, because that’s what the ponds seem to do with alarming frequency.

You’ve probably seen it, in some way, for years — a local pond seems suddenly crowded with algae — or there’s news of a “red tide” blooming at sea — as quickly as it forms, it seems to disappear.

In the Manhattan of algae test-ponds — the area around Mecca near California’s Salton Sea — an alarming number of ponds crashed, for example, around the time of the devastating San Diego County bushfires a few years back.

But it doesn’t have to be an extraordinary set of circumstances that threaten a pond system.

Because of the way algae is grown and produced in most algal ponds, they are prone to attack by fungi, rotifers, viruses or other predators. Consequently, algal pond collapse is a critical issue that companies must solve to produce algal biofuels cost-effectively. The issue was identified as a key component in the Department of Energy’s National Algal Biofuels Technology Roadmap.

To address the problem, this week a team at Sandia National Laboratories and the Arizona Center for Algae Technology and Innovation is debuting a suite of complementary technologies to help the emerging algae industry detect and quickly recover from algal pond crashes.

A brief side-trip into the creepy world of bioterrorism

Interestingly, the solution takes us, first, into the world of toolkits originally developed for combating the “unknown unknowns” problem in bioterrorism.

As then Secretary of Defense Donald Rumsfeld put it in 2002, “There are known knowns; there are things we know that we know. There are known unknowns; that is to say, there are things that we now know we don’t know. But there are also unknown unknowns – there are things we do not know we don’t know.”

In bioterrorism, of course — there are the usual suspects. Anthrax, smallpox, plague to name a few. But then there are the “enhanced agents,” genetically enhanced or manipulated in order to increase their virulence, their capabilities for creating destruction, or their ability to avoid detection.

Imagine, for example, a known agent that was re-engineered to spread as fast as a cold, was as hard-to-detect as HIV once was, and was as destructive as plague.

But as bad as all that is, it gets worse. There are the enhanced agents. Sandia researcher Todd Lane explains.

“An advanced agent could start with a benign organism that we’d have no interest in from a national security perspective and manipulate it into a virulent pathogen that is difficult to detect with current systems.” Here’s the problem: you only know you have a problem when the symptoms break out. “If a novel attack occurs and our detection systems fail, we have limited time in which to identify and characterize the organism to be able to offer effective treatment,” Lane said.

Consider this. A relatively recent outbreak of the Ebola virus in Uganda completely failed detection, even by advanced DNA-sequencing tools, because the virus had mutated so much — on its own — that it was unrecognizable. So you can imagine the threat. Especially when you consider the falling cost of genetic manipulation and the fast spread of powerful knowledge sets in the arts of the science.

Pond Crash Forensics

To combat this, Sandi developed a toolkit to address the RapTOR (Rapid Threat Organism Recognition) challenge — with a goal of 24 hour turnaround in characterizing new threats. . It was designed to serve as a tool to rapidly characterize a biological organism with no pre-existing knowledge.

It’s this toolkit that has now been applied to the real world challenge of characterizing algae pond crashes, a topic which picked up an $800,000 grant in 2010 from the DOE Biomass Program for a project on “Pond Crash Forensics.”

Using pathogen detection and characterization technologies developed under the RapTOR Grand Challenge, they are comparing the environmental conditions and metagenomes of algal samples taken from normal ponds to those taken from ponds that have undergone collapse.

“Pathogens and viruses fall into these ponds and can crash a pond overnight,” says Lane. “No one has identified many of the agents that are causing these pond crashes. You can’t develop countermeasures without understanding why something is happening. This is a complex problem with a lot of factors at play.”

Back to the Pond

So, back to our crash of algae and their self-destructing pond. Because the RapTOR technology is only one of three in the new algae pond-saving toolkit.

Sandia’s Tom Reichardt, a researcher who works in the lab’s remote sensing unit, led development of an online algal reflectance monitor through an internally funded project. The instruments are typically set up alongside the algal pond, continuously monitoring, analyzing the algae’s concentration levels, examining its photosynthesis and performing other diagnostics.

“In real-time, it will tell you if things are going well with the growth of your algae or whether it’s beginning to show signs of trouble,” said Reichardt.  However, he cautioned, while this real-time monitoring will warn pond operators when the ponds have been attacked, it may not be able to identify the attacker.

To help pinpoint the problems, a Sandia team led by researcher Todd Lane have developed a process to quickly and accurately identify pond crash agents through ultra-high-throughput sequencing using RapTOR.

Lane’s team also created a method for creating a field-ready assay for those agents, something that works quickly and is relatively inexpensive. They are applying SpinDx, a device developed by other Sandia/California researchers that can (among other features) analyze important protein markers and process up to 64 assays from a single sample, all in a matter of minutes.

Finally, a Sandia team led by researcher Jeri Timlin, in collaboration with the University of Nebraska’s Van Etten Lab, enhanced the RapTOR diagnostics by studying interactions of a certain virus with algal cells. Using hyperspectral imaging, they identified spectroscopic signatures of viral infections arising from changes in algal pigmentation. These signatures potentially could be exploited for early detection and subsequent mitigation of viral infections in algal ponds.

Sandia National Laboratories’ Tom Reichardt, left, and Aaron Collins, center, chat with John McGowen of the Arizona Center for Algae Technology and Innovation (AzCATI). Sandia has developed several complementary technologies to help the algae industry in detecting and recovering from pond crashes, and is making use of the AzCATI test-bed facility to collect data and apply its technologies. (Photo by Steffan Schulz)

Sandia technology being tested as part of AzCATI algae testbed project

Now that the core principles of pathogen detection and characterization technologies for pond crash forensics have been successfully proven, the next step will be to conduct more robust demonstrations.

Lane’s and Reichardt’s groups will be continuing their work as part of the Algae Testbed Public-Private Partnership (ATP3) led by Arizona State University (ASU), the first national algae testbed. The Sandia team will apply the technologies, collect more data and seek additional collaborations. The facility features algal ponds and closed photobioreactor algae cultivation systems of various sizes and serves as a hub for research, testing and commercialization of algae-based products.

The bottom line

Marcus Welby never did it so well — it looks like sick algae ponds have a strong set of tools to give “bedside” pond operators a chance to characterize illness and develop countermeasures, before the pond completely crashes. That’s good news.

Even better? Well, it would be a grand irony, indeed, if the biofuels paths to increased national security by reducing the dependence on foreign oil was made more possible by a toolkit originally developed by Homeland Security to combat low-cost bioterrorism from across the seas.