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Niches of Sunlight

The views expressed are those of the author and are not necessarily those of Scientific American.


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I’ve had an insanely hectic yet very important and productive time at work this month, so my blogging has fallen by the wayside. Next month I’ll be back to my normal blogging schedule, and just to kick things off here’s a post that first appeared in my old “Life of a Lab Rat” blog

Niches of Sunlight

In every environment there will be competition for resources, and there are generally two ways organisms deal with this; generalise or specialise. To generalise, you try to cope with as many different conditions as possible, so that if you get out-competed in one area you can try to cope with the conditions elsewhere. To specialise, you get damn good at using the conditions in your little niche, in the hope that you’ll be better than anyone else who comes along, and be able to out-compete them.

There are many resources that need fighting over, and in the sea one of the major ones for photosynthetic organisms is sunlight. Other nutrients such as nitrogen, phospherous and trace metals such as iron and copper can exist in different forms at different levels in the ocean (as shown below), but once you start getting below a certain depth, sunlight quickly becomes a finite and rapidly diminishing resource:

Diagram showing availability of nutrients at different depths.
Taken from the reference below.

Different organisms  cope with the lack of sunlight in different ways. Some (especially the larger algae species) have generalised, they contain a whole range of different light capturing pigments which can absorb a range of light wavelengths, including those in the darker depths. But the little photosynthesising bacteria Procholorococcus (which I mentioned in this post) which have the smallest genomes of all photosynthesising organisms, don’t have that option. Instead they have to specialise, so that different strains  within the species are adapted to different levels of light.

Work done by Rocap (paper reference below) looked at two different strains of Prochlorococcus: MED4 and MIT9313 (which I will just call MED and MIT). The MED strain was found only in the surface waters, while MIT was found much lower down; a phenomenon known as ‘vertical niche partitioning’. Despite their genomes differing by only 3%, and despite being technically the same species (although ‘species’ is an uncertain word in the world of bacteria) they have optimised themselves to completely different levels of not just light but also nutrients, trace metals and virus specificities.

Just a quick visual to make it clear - MED lives near the top of the water, MIT near the bottom.

MED (the one near the surface) has a slightly smaller genome than MIT, yet contains twice as many genes dedicated to high-light-inducible proteins, many of which seem to have arisen by gene duplication. It also has genes specialised for the nitrogen sources found near the surface of the water, and organic phosphates (which again are found predominantly on the surface). MIT on the other hand has fewer genes for ultraviolet damage repair (as light-damage is less of an issue deeper underwater!), but more light harvesting genes. This helps it to gather as much light as possible, despite being further below the surface. It’s also adapted for the nitrogen source found at the lower levels, and increased ability to use orthophosphate, rather than organic phosphates.

Both genomes have lost the ability for photoacclimatisation, that is the ability to change to suit different light conditions. By taking up vertical niche positions, they have forfeited the ability to change their response, meaning that a strict horizontal partition between them must be maintained at all times. Any Prochlorocuccus found at lower levels will be of the MIT variety, while those at higher levels will be MED. It’s even thought that there might be further strict niche partitioning; with different ecotypes of MED adapted to use different iron sources, or different temperatures.

For the photosynthetic organisms that inhabit it, seawater is more than just a blue shifting salty mass. It’s a whole range of niches and environments, partitioned in three dimensions depending on the surrounding conditions and nutrients.

Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, & Chisholm SW (2003). Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature, 424 (6952), 1042-7 PMID: 12917642

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

The views expressed are those of the author and are not necessarily those of Scientific American.





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