Within the genomes of these incredibly diverse eukaryotes, there is a huge amount of information that can help us understand the world around us - especially the mechanisms by which organisms can tolerate stingingly freezing environments such as the Southern Ocean, as well as days and nights that are months long.
Among the algae, a group of organisms which includes an unimaginable amount of genetically diverse and morphologically enthralling creatures, the diatoms are some of the most interesting.
Diatoms are scattered all over the planet and form a myriad of beautiful shapes known since Ernst Haeckel’s ‘Artforms in Nature’ due to their cells being enclosed in cell walls made of glass. These shells are so intricate and lovely that even the Victorians were known to arrange them into works of art. These shells are also useful as industrial catalysts.
What’s a diatom?
A diatom is a type of heterokont algae, which also includes organisms such as kelp and even water moulds (such as the disease that causes potato blight - Phytophthora infestans - related to brown algae). This is where the term algae actually, becomes quite confusing.
Algae include a whole range of living things spanning organisms that are plant and animal like at the same time, green or otherwise. Thus, nobody really knows what they are, which is why research into their genomes is of valuable importance.
In general, algae (in their various guises) show a combination of animal and plant-like features, which makes them tremendously hard to classify, but also makes them tremendously interesting to study - particularly when looking into how plants, animals and fungi came to be.
We can, at least, agree that the diatoms are often photosynthetically active - collectively producing more oxygen in the air than any other primary producer. They also have a urea cycle, which was only known to exist in animals - to indicate just how confusingly alike both plants and animals they really are.
Diatoms are scattered all over the planet and form a myriad of beautiful shapes, their cells being enclosed in shells made of glass. Credit: Barbol, Shutterstock
Diatoms are forever, forever, forever…
Diatoms are everywhere. From the pond in your back garden to the choppy, cold waters of the antarctic, there are diatoms. One such diatom is Fragilariopsis cylindrus, the focus of a recent study into adaptation to a freezing antarctic climate.
The antarctic is inhospitable for a number of reasons, not merely because it is freezing cold. The waters around Antarctica limit algal growth not only by low temperatures but also low concentrations of iron, which in turn limits photosynthesis and, therefore, their reproduction.
As the coldest place on earth, Antarctica only has summer and winter; with six months of daylight and six months of darkness. Along with large variations in temperature, reaching the lowest temperature ever recorded at minus 89.4 ͒C and the highest, 15 ͒C. Neither of which are particularly friendly towards maintaining a clockwork-like circadian rhythm.
Furthermore, these seasonal fluctuations also mean that Fragilariopsis inhabiting the frosty Southern Ocean around Antarctica spend the winter in the dark trapped within frozen sea ice, before thawing out to photosynthesise once more in the summer months.
Fragilariopsis cylindrus is so successful at tolerating the freezing waters of the Southern Ocean that it is used as an indicator of polar waters in general, i.e. if there’s lots of it, the water is probably pretty nippy.
To put up with this, these cold-embracing algae must have harnessed some interesting adaptations to help them cope. To find out more about this, researchers in Norwich, and Walnut Creek in the US decided to compare them genetically with more temperate algal species, in order to find out more about what makes them bask when others might shiver.
Ironing out the genome.
More often than not, now that we have the perks of next generation genome sequencing available to us, it’s much quicker to find what might help an organism adapt to certain conditions through identifying changes in an organism’s genetic code.
Thus, with the help of some high-quality NGS thanks to the Platforms & Pipelines and Clark Groups at EI, the PacBio-assembled F. cylindrus draft genome did indeed hint at how its icy adaptations came about.*
One important difference between F. cylindrus and its more temperate diatom counterparts was that, in terms of metal-binding proteins, it was enriched in copper and zinc-binding proteins rather than iron binding proteins.
This makes sense, as in the low-iron environment of the Antarctic, F. cylindrus has to find a way to keep up photosynthesis. It’s thought that, perhaps, the extra copper-containing proteins in Fragilariopsis might help with the electron transport necessary for photosynthesis, without having to rely on extra iron.
The zinc-binding proteins are also interesting, as they appear to be abundant in F. cylindrus. Zinc, apparently, is particularly abundant in the surface waters of the Southern Ocean, so you might expect there to be lots of zinc-binding proteins in the algae that live there.
Additionally, however, some of these proteins appear to have arisen in the algae from horizontal gene transfer from bacteria - which is always an interesting topic to throw into the mix when trying to explain the evolution of life on earth.
Importantly, many of these proteins could well have a role in stress response, which is a point of immediate concern for any organism faced with the probability of being cryogenically (frozen) concealed for months at a time.
One group of such proteins, for example, is the group of antifreeze proteins, which help them to survive the transition from sea water to sea ice when temperatures drop below the freezing point in autumn.
In general, algae (in their various guises) show a combination of animal- and plant-like features, which makes them tremendously hard to classify, but also makes them tremendously interesting to study - particularly when looking into how plants, animals and fungi came to be.
Credit: Barbol / Shutterstock.com
What turns them on?
Any study into environmental adaptations should include the analysis of RNA, which shows us the genes that are switched on and off in an organism in response to stress. As such, the RNA profile (the transcriptome) of Fragilariopsis was analysed under varying conditions including darkness, low iron and freezing.
Interestingly, the biggest switch occurred in the response to darkness, with around 60% of all genes showing changes in regulation. When considering an organism that requires light to feed itself, however, perhaps this isn’t all-too-surprising.
The RNA-sequencing experiments also revealed that another method behind the adaptive nature of F. cylindrusis its highly divergent genes, which appear to have undergone “positive selection” in recent years (evolutionarily speaking, coinciding with the start of the last glacial period 110,000 years ago).
Amid a vastly diverse gene pool, Fragilariopsis appears to have been able to acclimatise so well to annual freeze-thaw cycles, in what is essentially an evolutionary positive feedback loop. The genes that favour the adaptation to the environment in which the organism finds itself are increasingly favoured, and thus, eventually, exist in a greater proportion, allowing greater numbers of the organism to thrive.
The importance to algae for all of the oxygen-breathing life on earth is clearly apparent.
However, it's studies like this which shed light on how incredibly diverse these fascinating creatures are - all the more interesting when we consider that algae are little half-plant, half-animals scurrying in a murky mire of phylogenetic confusion.
The more we can find out about these organisms, the more we can begin to understand the processes that guide their evolution - and can give us insights into the biology of all eukaryotes on earth.
Furthermore, in a world undergoing some of its most rapid changes since before the ice cores can tell us any differently, the more we know about how organisms can tolerate fluctuating environments, the better.
*The Sanger genome assembly and annotations used in this study are available via the JGI genome portal at http://genome.jgi.doe.gov/Fragilariopsis_cylindrus.