Benthic algae: the iPhone 4S of algae?

Introduction: the next generation of-next-gen biofuels
Algae are often billed as "next-gen" biofuels, because they're expected to surpass the productivity and envitronmental sustainability of first-generation biofuels based on corn and soy.  However, new research published in the journal AMB express suggests there's an even newer generation of biofuel on the horizon.  Will biofuels soon outpace Apple and its iPhones in terms of product cycles?  Only time will tell.

The problem: too much water
One major roadblock for producing algal biofuel is separating algae from the water in which they grow. To collect algae from current systems strategies like filtration, centrifugation, gravity, and evaporation are used.  Each of these approaches has its drawbacks, which result in increased cost of production.  Filters are expensive and need to be cleaned.  Centrifugation takes a lot of energy.  Gravity and evaporation take time and space that could be used for growing more algae. 

It takes a lot of energy to separate the algae from the water in this raceway system.

The new kid on the block: benthic cyanobacteria

Not all algae, however, grow as single cells in the water that need to be scooped up in some way.  Some algae scoop themselves up into large biological mats.  In July, three researchers from Cawthron Institute in New Zealand investigated three different species of benthic cyanobacteria that harvest themselves!  What are benthic cyanobacteria, you ask? Benthic organisms come from the seafloor or lake bed (the benthos). Cyanobacteria used to be known as blue-green algae until someone realized that they're in fact bacteria and not algae at all.  That said, they have very similar properties to eukaryotic algae.  For instance, they can turn CO2 into sugar and lipid using sunlight.  They can store other nutrients for use.  They are a potential feedstock for biofuels.

What makes these particular algae unique is their ability to grow in easily collectible mats.  However, as I've mentioned in previous posts, many wild organisms that look useful don't necessarily grow in culture.  Indeed most organisms (over 99%) don't grow in culture.  The challenge before these authors was finding the culture conditions that would produce the maximum amount of bacteria.

A mat of benthic cyanobacteria from New Zealand that has collected on a rock

The hunt for the substrate: what's handy?
The main challenge before the authors was finding a substrate for the bacteria to grow.  In order to figure this out, they literally just looked around the lab.  As you can see from the figure below, the authors just stuck common lab items into bioreactor bags and hoped something would stick.

The various conditions researchers tried to grow this new form of algae.  Panels A and B are bioreactors held horizontally or vertically.  Panel C is a bioreactor bag with silicone lab tubing.  Panel D is clearly just a bottle brush in a bag.  Panel E is another piece of silicone tubing folded in on itself.

The result: great green glop!
Surprisingly, the authors were able to find optimal growth conditions just by grabbing what's around.  It turns out the looped silicon grew 2 times more cyanobacteria than the other growth strategies.  That said, the final yield even from the best bioreactor was 7 times lower than growing normal algae in an open pond without CO2 amendment and far lower than growing normal algae in a photobioreactor.  I guess that's what makes this organism a next-generation next-gen biofuel.  If further optimization can occur (through improved culture conditions, genetic manipulation, further bioprospecting, or more), perhaps this cyanobacteria will outperform todays best algae.  

The cyanobacterium Phormidium autumnale after 36 days of growth in a photobioreactor in and out of water (a and b).

Shedding some light on dark organisms

INTRO: dark organisms defined

Physicists have dark matter.  Biologists have what I like to call dark organisms.  These are the myriad organisms that cannot grow in culture, and thus remain relatively unstudied. Consider that some estimates suggest that only 1 in 1000 bacteria can be successfully grown in the lab right now.  That leaves a lot of work to do to to uncover the literally millions of organisms producing antibiotics, anti-cancer therapeutics, and biofuels of tomorrow.

COAL-BED METHANE: a biological process in need of refinement

Since the 1980's, it's been known that some of the natural gas found in coal deposits came from bacterial organism (Schoell 1980).  Of late, companies like synthetic genomics and Luca technologies have developed chemical mixes that can stimulate the bacteria living in coal deposits and get them to eat more coal and turn it into methane.This is a huge potential source of (relatively) clean energy from coal.

Consider, however, that many extreme organisms converting coal into cleaner methane die when moved from the nutrient-poor depths of a coal mine to the nutrient-rich surface, or to the lab. 

We need to understand and grow the organisms producing our future methane, if we want more of this energy.

A GENETIC LOOPHOLE: why culture the organism, when you can get the sequence anyways?

A recent paper in the Journal of Bacteriology turned me on to a new solution to the problem of studying unculturable bacteria.  Why not just sequence the bacteria where they live?

Now that we have next-generation sequencing technology and the complete sequence of almost every model organism, it is possible to rapidly sequence a small amount of starting DNA collected from the wild.

In this JB paper.  The authors collected about a gallon-and-a-half of water from an offshore oil field, isolated the DNA, and assembled the genome of an entirely new species found growing in that oil field. They compared the DNA sequences they collected to a reference organisms sequence grown in the lab.  when they assembled all of their DNA sequencing data, they found a 1.6 million base sequence representing a new strain of the species Methanococcus maripaludis called X1. 

While the authors found some inconsistencies and point mutations in their data, they suggest these results do not indicate multiple strains in their water, but rather technical errors they were able to sort out manually.  Either way, the data from strain X1 will lend insight into the various genes present in nonculturable strains of this organism.

THE NEXT STEP: using these genes in culture

It's an exciting step to see a new strain of an organism sequenced without culturing it first.  It's a big step forward to shedding light on these dark organisms.  The next step will be when we successfully use the genes from these organisms to produce new antibiotics, therapuetics, and fuels. 

REFERENCES

 Schoell M. 1980. The hydrogen and carbon isotopic composition of methane from natural gases of various
origins. Geochim. Cosmochim. Acta 44:649–61

Wang X, Greenfield P, Li D, Hendry P, Volk H, Sutherland TD. Complete Genome Sequence of a Nonculturable Methanococcus maripaludis Strain Extracted in a Metagenomic Survey of Petroleum Reservoir Fluids. J Bacteriol. 2011 Oct;193(19):5595. PubMed PMID: 21914896.