Guest posting: Let’s crowdfund a fern genome that will blow your mind

June 16, 2014

Following our efforts encouraging open-science projects, such as the community funded “Peoples Parrot” and OpenAshDieback, today we have a guest posting from Fay-Wei Li and Kathleen Pryer from the Department of Biology at Duke University covering a crowdfunding effort to sequence the Azolla genome.  They have already raised over $4,000 and have 25 days remaining until their deadline, so if you find the project interesting, there is time still to contribute on Experiment.com.

We need a fern genome.

Why? Because considering the 470 million year history of plants on land, most species belongs to bryophytes, lycophytes, ferns and gymnosperms, which eventually yielded to the infamous flowering plants 90 million years (Myr) ago. Ferns, the third largest of these five radiations-and the sister group to all seed plants-is the only lineage for which a reference genome has not yet been sequenced. That doesn’t sound right, does it? Without a fern genome, we cannot fully comprehend the processes that govern the evolution of plant genes and genomes, and the patterns underlying major evolutionary transitions in land plants will still remain elusive.

Important guidelines in selecting candidates for genome sequencing have included economic relevance to humans, ability to answer important biological questions, and a small genome size. Azolla, an inconspicuous aquatic fern, passes all three criteria with flying colors. In this blog post, we will show you how Azolla genomic studies can not only drastically improve our understanding of plant evolution, host-symbiont interactions and nitrogen metabolism, but also have broad implications for sustainable agriculture and alternative biofuel production. We also present our citizen science crowdfunding attempt to initiate the Azolla Genome Project.

http://vimeo.com/96967106

Azolla is a ‘superorganism’
Azolla is a most unusual fern. It is a minute, aquatic plant that floats on the surface of ponds and lakes, bearing little resemblance to a typical fern. In addition, Azolla’s 740Mb genome is tiny compared to other fern genomes (740Mb vs. >10Gb), making Azolla an ideal first genome to be sequenced in ferns. Azolla is also a superorganism: within specialized cavities in each of its tiny leaves, Azolla harbors the nitrogen-fixing cyanobacterium Nostoc azollae. The Azolla-Nostoc interaction is unique among known plant-bacteria endosymbiotic associations in that the symbiosis is maintained even during sexual reproduction, whereby the Nostoc cyanobiont is vertically transmitted to subsequent generations. Because of such vertical transmission, the cyanobiont phylogeny mirrors the Azolla species phylogeny.
Azolla and Nostoc have co-evolved for nearly 100 Myr. Nostoc has entirely lost its autonomy, as it cannot be cultured when isolated from the host plant. Recent sequencing has revealed that Nostoc azollae is undergoing genomic downsizing, suggesting it might be in the early stages of evolving into a plant organelle devoted to nitrogen fixation. Loss-of-function in the cyanobiont is most prominent in genes related to nutrient uptake and metabolism, response to environmental stimuli and DNA repair. However, function has been retained in key symbiotic processes, such as nitrogen-fixation and cell differentiation.
Nevertheless, this somewhat well characterized Azolla-Nostoc symbiosis is just the tip of Azolla’s microbiome iceberg. In addition to Nostoc, an entire community of other bactobionts exists within Azolla’s specialized leaf cavities, including other Nostoc species, Arthrobacter, Agrobacterium and Corynebacterium. Interestingly, some of these non-Nostoc symbionts appear to also have nitrogen-fixing capabilities, suggesting that they may contribute to Azolla’s capacity for nitrogen fixation. However, this microbial community is very poorly characterized: the diversity and identity of these other bacteria, their degree of interaction with their host, their mode of inheritance, and most critically, their role in enabling Azolla’s ‘superpower’ (as you will see next), have not yet been established.

This superorganism’s ‘superpower’
Why should we care about Azolla (other than for its fascinating coevolution story with its microbiome)? We believe that Azolla has enormous, yet long-overlooked, green potential. As we all know, we have screwed up our planet. The climate is getting hotter, water is getting less abundant and dirtier, energy is in crisis, and food production is unable to keep up with growing population demands. To help us get out of this situation, we need to learn how nature “does what it does” naturally. One peek into the buried Azolla literature and you would be amazed by its potential to help bring down atmospheric CO₂ level, clean up contaminated water, provide alternative biofuels, and boost sustainable agriculture—a perfect storm!

Global warming and biofuels—Fossil data from the Arctic Ocean show that about 50 Myr ago, there was an enormous Azolla bloom spanning nearly a one million-year-interval, known as the “Arctic Azolla event”. It is estimated that Azolla covered 4,000,000 km² of freshwater in the Arctic, which translates into over 10¹² tons of carbon sequestration. The massive atmospheric CO₂ drawdown by Azolla during this period cooled the earth, and shifted the Early Eocene greenhouse world towards our present icehouse climate.
Can Azolla do it again? Azolla is fast-growing (capable of doubling its biomass every other day), easy to harvest, contains low-levels of lignin, and does not compete for arable lands with other crops, conditions that are perfect for biofuel-based, alternative energy production. Perhaps we can summon Azolla again to help us combat global warming?

Phytoremediation and wastewater treatment—Water shortage is undoubtedly one of the most serious crises we are facing today. The availability of potable water has been greatly impacted by industrial and agricultural pollution. In the past two decades, Azolla has been shown to be capable of hyperaccumulating a great variety of heavy metal pollutants—arsenic, gold, cadmium, chromium, copper, lead, mercury, nickel—to as much as 2% of the dry weight. In addition, Azolla can degrade 60-90% of bisphenolA (BPA) from aqueous solution, and when tested in swine wastewater, it is able to effectively decontaminate superfluous ammonium and phosphorus, thereby suppressing algal blooming and eutrophication.
Azolla’s astonishing ability to remove various hazardous pollutants, grow rapidly and be easily harvested; makes this fern a very promising phytoremediation agent for wastewater treatment.

Nitrogen fixation and sustainable agriculture— to feed the world’s growing population, we will need roughly 200 million tons of industrially produced, nitrogen-rich fertilizer by 2015, a process that will consume vast amounts of fossil fuel and greatly exacerbate our CO₂ problems. To make things even worse, over 20% of these applied nitrogen fertilizers will runoff into delicate water systems, fueling phytoplankton blooms and causing extensive ‘dead zones’. Azolla—with its symbiotic, nitrogen-fixing microbiome—offers an alternative and much more sustainable solution. Compared to the more familiar legume-Rhizobia system, the Azolla–Nostoc symbiosis fixes almost three times more nitrogen per hectare. Asia’s farmers have known this for thousands of years, growing Azolla with rice to bolster its productivity. Indeed, a recent field experiment has shown that incorporating Azolla, duck and fish into rice farming can more than double the net revenue.
Rice will continue to be one of the most important crops in the world. With the recent publication of 3,000 rice genomes, we can definitely foresee a significant leap in rice genetic breeding. However, here we want to also champion Azolla—rice’s best companion—that, in addition to enhancing rice’s productivity, can also bring sustainability to the table.

Crowdfunding the Azolla Genome Project
We hope we have persuaded you that Azolla comprises a gamut of fascinating aspects worth exploring, not just about its biology, but also its relevance to humanity and the global environment. We plan to generate a draft genome for Azolla and complete metagenomes for all its associated microbiota. Such “omics resources” will be the first step toward unlocking and harnessing this superorganism’s superpowers. We initiated a crowdfunding campaign to kickstart this Azolla Genome Project. It is an experiment, but our citizen science approach has allowed us to reach out and directly engage with the general public. So, please check us out when you see us navigating through the social network!