journal club

Putting Microbes to Work in Ocean Science

What if we could use diatoms to monitor ocean chemistry and biology?

The closest oceanography has come to its very own Dr. Strangelove was when Moss Landing Marine Laboratory’s Dr. John Martin joked, “Give me half a tanker of iron, and I’ll give you an ice age.” Iron is, in fact, a key limiting nutrient in much of the world’s oceans, required for growth and productivity of its planktonic life. Of course, marine plankton are major controllers of the global climate; their productivity means more photosynthesis, and more photosynthesis means more greenhouse gases removed from the atmosphere. This is the process Martin referred to with his ice age. If iron is a rare nutrient limiting primary productivity, add enough as an environmental supplement and you could end up with a globe-cooling plankton bloom. It’s more complicated than that, of course, but iron fertilization remains a point of interest among biogeochemists, oceanographers, and climate scientists today.

In their paper Development of a molecular-based index for assessing iron status in bloom-forming pennate diatoms, Marchetti et al. (2017) looked for a quick trick in assessing iron levels in ocean samples. They designed an easily measurable index to improve upon the current cumbersome method, and in doing so, they developed a tool that connects ocean chemistry to the ecosystems it supports. Let’s take a look at their efforts.

An Index for Everything

This isn’t the first time an important index measurement has been the product of an ocean sciences paper.

Oceanographers have long been obsessed with indices to inform their studies, looking for general rules they can apply to get a sense of what’s off in any given marine region. The Redfield Ratio was proposed in his classic 1934 paper, Alfred Redfield proposed an index describing the proportions of the three main nutrients found in seawater (and living things, for that matter). For every 140 carbon atoms, there are 20 atoms of nitrogen, and 1 atom of phosphorus.

That’s right, phosphorus is a rare – and highly competed for – nutrient in most of the world’s oceans. The ratio has been debated ever since, as of course the entire marine ecosystem doesn’t follow it perfectly. But researchers have since added oxygen to the mix (another common player in organic matter), with an updated ratio (in grams, not moles) of P:N:C:O2 of 1:16:140:172.

Those numbers may well mean nothing to you. But they are a nice theoretical standard, and it’s easy to check seawater samples in any particular spot and get actual experimental data to corroborate it. When the experimental data differs from this ratio, it tips oceanographers off to the biological activity in that region. If nitrogen fixers are active there, the ratio will be skewed for more nitrogen. If denitrifying plankton dominate, Redfield Ratio tips in the other direction. With one index, you can quickly assess the state of local microbial ecology.

Checking Iron with Genetics

Redfield Ratio is an index for scientists keeping an eye on carbon, oxygen, nitrogen, and phosphorus. What about iron? It’s another key nutrient, and we can infer plenty about the biology, chemistry, even geology of a marine ecosystem based off of it.

For their study, Marchetti et al. focused on the common marine diatom, Pseudo-nitszchia. This lovely glass pennate creature can adapt to watery worlds where iron is limited or abundant. And like any other microbe, it adapts by changing the expression of related genes.

Researchers can check how genes change under varying conditions by looking at transcriptomics.

The Central Dogma – DNA is transcribed into RNA, and RNA is translated into proteins.

You can get a transcriptome by collecting and reading RNA. If it’s RNA, you know it’s actively being transcribed – it’s for a protein the cell needs around. In this case, researchers wanted to know what genes turn on and off when Pseudo-nitszchia is exposed to plenty of iron, or has to fight for it.

Now, most of the transcriptome doesn’t change. In both of these conditions, most of the “on” genes are for basic living arrangements, and most of the “off” genes are for special circumstances only. However, they did notice two transcripts with wildly different levels depending on the iron concentration. This is exactly what they were looking for – two genes, one that turns “on” when iron limitation gets rough, and one that turns “off.”

Now, iron is very important to primary producers. Iron is necessary for shuffling carbon and nitrogen around, and is associated with chlorophyll concentration and photosynthesis efficiency. The biochemistry here is important to the cell, so there should be a few iron-related genes to choose from.

Ferritin (FTN) was one of the genes they found. FTN codes for a protein that stores iron when there’s plenty of iron around. Under iron limitation, this gene turns off. The other gene was the aptly named iron-starvation-induced protein 2a (ISIP2a), and it turns on under iron limitation. ISIP2a has only recently been discovered, but we do have a few guesses for its job. It appears to concentrate iron near the cell membrane, possibly to help iron uptake.

As RNA transcripts, both of these have the advantage of pronounced concentration differences when iron is limited. That means, for any given seawater sample, you can extract the Pseudo-nitszchia transcriptome, measure these two transcripts, and check their differences. This ratio of ISIP2a:FTN acts as an iron indicator. It’s the index proposed by the researchers. It’s not without some inevitable complications (as happens in biology – those cells can be fickle). However, it improves upon current iron measurement methods and is a promise new tool in biogeochemistry.

References

Marchetti, A., Moreno, C. M., Cohen, N. R., Oleinikov, I., deLong, K., Twining, B. S., Armbrust, E. V., & Lampe, R. H. (2017). Development of a molecular-based index for assessing iron status in bloom-forming pennate diatoms. Journal of Phycology, 53(4), 820–832. https://doi.org/10.1111/jpy.12539

Redfield, A. C. (1934). On the Proportions of Organic Derivatives in Sea Water and Their Relation to the Composition of Plankton. University Press of Liverpool, James Johnstone Memorial Volume, November, 1767–192.

Takahashi, T., Broecker, W. S., & Langer, S. (1985). Redfield ratio based on chemical data from isopycnal surfaces. Journal of Geophysical Research, 90(C4), 6907–6924. https://doi.org/10.1029/JC090iC04p06907

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