Nicole Nogoy

**Following our efforts encouraging open-science projects, such as the
community funded ["Peoples
Parrot"](http://www.bio-itworld.com/2012/09/28/peoples-parrot-first-community-sponsored-genome.html)
and
[OpenAshDieback](http://blogs.biomedcentral.com/gigablog/2013/02/13/open-science-versus-ash-dieback-and-the-tweenome-revisited/),
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](https://experiment.com/projects/azolla-a-little-fern-with-massive-green-potential).**

::: {#attachment_1131 .wp-caption .alignright style="width: 310px"}
[![IMG_1562_reduced](http://gigasciencejournal.com/blog/wp-content/uploads/2014/06/IMG_1562_reduced-300x204.jpg "Azolla fern"){.size-medium
.wp-image-1131 loading="lazy" decoding="async"
aria-describedby="caption-attachment-1131" width="300" height="204"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/06/IMG_1562_reduced-300x204.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/06/IMG_1562_reduced-768x523.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/06/IMG_1562_reduced-1024x697.jpg 1024w"
sizes="(max-width: 300px) 100vw, 300px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2014/06/IMG_1562_reduced.jpg)

Photo courtesy of Fay-Wei Li
:::

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](https://experiment.com/projects/azolla-a-little-fern-with-massive-green-potential).*

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)](http://www.cell.com/trends/plant-science/abstract/S1360-1385(02)02375-0?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1360138502023750%3Fshowall%3Dtrue?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1360138502023750%3Fshowall%3Dtrue)*,
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](http://link.springer.com/chapter/10.1007%2F978-90-481-9449-0_11)*.
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](http://link.springer.com/article/10.1007%2Fs001220051323).  
*Azolla* and *Nostoc* have [co-evolved for nearly 100
Myr](http://www.jstor.org/discover/10.1086/519007?uid=3738776&uid=2&uid=4&sid=21104161608677).
*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](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011486).
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](http://link.springer.com/chapter/10.1007%2F978-90-481-9449-0_11)
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](http://www.ncbi.nlm.nih.gov/pubmed/1785936). 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 CO~2~ 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"](http://www.nature.com/nature/journal/v441/n7093/abs/nature04692.html).
It is estimated that *Azolla* covered 4,000,000 km^2^ of freshwater in
the Arctic, which translates into [over 10^12^ tons of carbon
sequestration](http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4669.2009.00195.x/abstract;jsessionid=24622A2410F9E806AC1396862A536A1D.f02t02?deniedAccessCustomisedMessage=&userIsAuthenticated=false).
The massive atmospheric CO~2~ drawdown by *Azolla* during this period
cooled the earth, and shifted the Early Eocene greenhouse world towards
our present icehouse climate.  
[Can ]{style="line-height: 1.5em;"}*Azolla*[ do it again?
]{style="line-height: 1.5em;"}*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 ]{style="line-height: 1.5em;"}[perfect for
biofuel-based, alternative energy
production](http://onlinelibrary.wiley.com/doi/10.1111/nph.12708/abstract){style="line-height: 1.5em;"}[.
Perhaps we can summon ]{style="line-height: 1.5em;"}*Azolla*[ again to
help us combat global warming?]{style="line-height: 1.5em;"}

***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](http://link.springer.com/article/10.1007/s13280-011-0159-z). In
addition, *Azolla* [can degrade 60-90% of bisphenolA
(BPA)](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018667/) 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](http://www.biotechnologyforbiofuels.com/content/7/1/30).  
*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
CO~2~ 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](http://link.springer.com/article/10.1007%2FBF00020426). 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](http://www.ncbi.nlm.nih.gov/pubmed/22957173).  
Rice will continue to be one of the most important crops in the world.
With the recent publication of [3,000 rice
genomes](http://www.gigasciencejournal.com/content/3/1/7), 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](https://experiment.com/projects/azolla-a-little-fern-with-massive-green-potential)*.
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!

The post [Guest posting: Let's crowdfund a fern genome that will blow
your
mind](http://gigasciencejournal.com/blog/guest-posting-lets-crowdfund-a-fern-genome-that-will-blow-your-mind/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


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.

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

Cameron Neylon

Image via Wikipedia The Royal Society is running a public consultation exercise on Science as a Public Enterprise. Submissions are requested to answer a set of questions. Here are my answers.

 1. What ethical and legal principles should govern access to research results and data?

Rogue Scholar Beiträge

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

Submission to the Royal Society Enquiry