Thomas' Plant-Related Blog

On plant science. Mostly.

Is climate change affecting phytoplankton?

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Phytoplankton—single celled green floaters—fulfil the same role in the oceans as plants do on land. They’re the basis of the food chain, capturing energy from sunlight, and eventually feeding just about everything else. So the news that they’ve declined by about 40% since 1950 (Nature News) is rather worrying. Let’s take a look at where the number came from.

Black and white disk, suspended above water.

A Secchi disk. Photo from eutrophication&hypoxia (flickr)

The standard way of finding the amount of phytoplankton in seawater is to measure the concentration of chlorophyll, the green pigment used in photosynthesis. Essentially, you can just test how green the water is, although modern methods are a bit cleverer. Using satellites, you can even remotely measure vast areas of ocean. But people didn’t make those measurements much until the 1960s (and not with satellites until 1979). So the researchers combined them with an even simpler method, which has been done a lot since the 1930s. The ‘Secchi disk’ is lowered into the water until it can no longer be seen, giving a measure of how clear the water is. After throwing out measurements near the shore, where mud can reduce visibility, they fit pretty well with the chlorophyll measurements.

What did they find? Well, the number the media picked up on was the global average 1% decline per year. That’s one percent of current levels, so working back gives you just under a 40% drop since 1950. That average, though, hides quite a bit of variation in the actual change:

Graph of the historic changes in chlorophyll in eight regions of the global ocean.

Changes in phytoplankton (chlorophyll concentration). Based on a figure in the paper, with minor modifications.

It looks like there’s a clear decline in the Atlantic ocean and the polar oceans, a smaller decline in the Pacific, while plankton actually increased in the Indian ocean. The authors go one step further, breaking it down into large grid squares. That shows still more variation, but without a clear pattern, at least to my eye.

I mentioned a link with climate change. It works like this: when you heat a pan of water on a stove, you get convection currents, as warm water rises, cools, and sinks again. But the oceans are mostly heated from the top, by sunlight, which means a layer of warm water forms, sitting on top of a huge depth of colder water. Phytoplankton can only grow near the surface, because they need sunlight, but they quickly use up the nutrients there, and then need water mixed in from the depths to grow. As a result, regions of upwelling water, such as off the coasts of Peru and Antarctica, have particularly rich sea life. The ocean currents that drive them aren’t expected to stop any time soon, but warmer temperatures at the surface could be reducing smaller scale mixing.

This isn’t just conjecture. The scientists separated the year-by-year variation in plankton levels from the overall trends, and compared that variation to various ocean ‘oscillations’. These are roughly regular patterns in temperature and pressure, the best known of which is the El Niño/Southern Oscillation in the Pacific. In most areas with oscillations, there was less plankton in warmer years (the pattern didn’t fit for the North Indian ocean, perhaps due to the effects of the monsoon rains).

I’m a bit surprised, reading the paper, that they didn’t explore any of the other things that could be affecting the plankton. There’s a brief list of possible factors, including nutrients coming from the land, ocean circulation, and the effects of other organisms in the sea, but then only the surface temperature and the resulting ‘mixed layer depth’ are given any discussion at all.

If phytoplankton are on the decline due to global warming, that’s not just bad news for the algae. As I described above, almost* everything in the oceans ultimately relies on phytoplankton. They’re also a key part of the carbon cycle, removing CO2 from the air. That leads to a positive feedback: as we release more CO2 and warm the earth, we also slow down its absorption by life in the oceans.


Boyce, D., Lewis, M., & Worm, B. (2010). Global phytoplankton decline over the past century Nature, 466 (7306), 591-596 DOI: 10.1038/nature09268

*Treasure your exceptions: some things living at hydrothermal vents can get all their energy from dissolved chemicals.


Written by Thomas Kluyver

6 August, 2010 at 11:56 pm

New crops: perennial grains?

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Most of our staple crops are annuals—plants that grow from seed, produce the next generation of seeds and then die, all in one year. In particular, the ‘big three’ crops, rice, wheat and maize, are all annuals. What would life be like if we instead grew perennials—plants that last more than one year? No more yearly ploughing and sowing.

Pear orchard

Pear orchard in the US. Photo by victorhansonsmith (flickr)

First things first: we’ve already got plenty of perennial crops. Many fruits, such as apples, grapes and kiwis, grow on trees and vines, and plants like the tomato can grow as annuals or perennials. But they’re luxuries, not our daily bread. The cereals and pulses that we depend on are almost all annuals. Read the rest of this entry »

Written by Thomas Kluyver

28 July, 2010 at 11:02 pm

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Why moss blows smoke rings

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Science via Youtube today. Let’s start with some smoke rings.  They go an impressively long way—much further than a simple puff of smoke fired with the same force would:

So, why might a moss need to do the same thing?

It’s all about spores. Mosses spread by spores, a bit like microscopic seeds. For peat moss (Sphagnum), growing low on the ground in  bogs, the challenge is to catch the wind, getting its spores high enough that eddies in the air carry them away. It launches them, after building up 2–5 times atmospheric pressure behind them, but that by itself wouldn’t be enough: like a puff of smoke, the dust-like spores would quickly slow down, staying in the still air near the ground, and settling back to the ground. So they blow tiny smoke rings:

Could other plants use the same trick? Spores, pollen and the smallest seeds (such as those of orchids) could all potentially be ‘puffed’ like this. But most plants are high enough to catch the wind easily: the authors reckon it’s only about 10cm up in the bogs where peat moss lives. White mulberry, recently featured on QI as the ‘fastest thing in biology’, flings its pollen with a catapult mechanism (here’s the paper for subscribers) that couldn’t generate a ring vortex.

Maybe the best place to look would be fungi, some of which face a similar challenge to the peat moss when launching their spores. There are other ways to approach it, though. Take a look at these Pilobolus fungi, which use a ‘water pistol’ approach to launching spores (this paper is open access). Interestingly, the pressure they use to launch is similar to that in the moss.

Finally, to round off this post of Youtube science, let’s take a closer look at vortex rings (the technical name for smoke rings). They hold together by rolling through the air on the outside, while the inside’s moving forward faster. Here it is with ink in water:


Whitaker, D., & Edwards, J. (2010). Sphagnum Moss Disperses Spores with Vortex Rings Science, 329 (5990), 406-406 DOI: 10.1126/science.1190179

Written by Thomas Kluyver

24 July, 2010 at 1:55 pm

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Introducing ‘Pied Paper’

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If you’ve ever tried to read a journal paper on screen, you’ll know that it’s not always easy. With widescreen monitors now common, the text you’re trying to read ends up either as a long, narrow column surrounded by menus and sidebars, or spread out so wide that you can’t comfortably read the long lines. You could download a PDF, but since they’re designed to be printed, it’s often clumsy to read them on screen.

A scroll (the Torah)I wondered if we could lay a paper out to make better use of a large monitor. Using a relatively new feature in browsers, I’ve experimented with putting papers into multiple columns, continuing off the screen to the right, somewhat like an old fashioned scroll. The prototype got enough interest that I’ve (finally) made a tool to reformat papers ‘live’.

How to get it

If you’re using Firefox, you’ll need an add-on called Greasemonkey to run Pied Paper. Install it from here, then restart Firefox. Chrome (and possibly Opera) can use Pied Paper without this step. (It won’t work in Internet Explorer at all, I’m afraid)

Then get Pied Paper (click the install button on that page).

How to use it

Pied Paper currently works on:

When you load the full text (HTML) of a paper on one of those sites, Pied Paper will recognise it, and automatically reformat it. At present, if you want to go back to the original format, you’ll need to disable Pied Paper (in Firefox, use the Greasemonkey monkey icon in the bottom right), and reload.

Please don’t hesitate to let me know if you encounter any problems.


Although this is a tool that I hope you’ll find useful, it’s not exactly polished. Part of this is down to the script, and if people express interest in the idea, I’ll look at using more sophisticated tools to deal with it. Part of it is down to the browsers: multi-column support is quite new, and hopefully over the next couple of years, it will mature.

For a similar tool to remove clutter, without the unusual scroll-like layout, try Readability (a project I have nothing to do with).

Finally, if you read journal papers often, allow me to plug Refzap, a tool I made for quickly looking up citations.

Written by Thomas Kluyver

23 June, 2010 at 6:49 pm

Posted in Computers

Glomalin: Carbon stored in a protein you’ve probably never heard of

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What’s soil made of? Take out the chunks of roots and twigs, take out the particles of minerals, and what are you left with? What makes it soil, brown and lumpy, rather than something like fine sand? It’s a mixture of organic matter: stuff produced by things living in or on the soil, that can’t readily be broken down, and it’s attracting attention now because it stores quite a lot of carbon across the world. One important part is ‘humic acid’, a mix of complex acidic chemicals from decaying plant matter. ‘Humin’ is a generic name for the stuff that won’t dissolve. But in the last decade, another important component has been found, a tough protein called glomalin.

A root, highlighted green showing where glomalin is

Glomalin, highlighted in green, around mychorrhizae (thin threads and blobby spores) growing on a root (thick part). Image by Sara Wright, USDA.

Most plants team up with fungi to get nutrients, especially phosphorus, from the soil. Fungal threads, or hyphae, can be much thinner than plant roots, so they can explore soil more efficiently. Those fungi are called mycorrhizae, and the most important group of them, the arbuscular mycorrhizae, are responsible for producing glomalin, which is possibly important to their structure. And although the fungal threads die and are replaced constantly, glomalin seems to last for years in the soil.

Besides containing carbon itself, glomalin also helps to glue together organic matter in the soil, slowing its decomposition, and so keeping more carbon in the soil and out of the atmosphere.

Different soils have different amounts of glomalin. In farmland, for example, leaving soils unploughed, as in ‘no till’ cultivation, allows glomalin to build up. Glomalin molecules also include iron, and there are hints that soils rich in iron might hold more of it.

In Hawai’i, scientists found that older soils (up to 4 million years old) had more glomalin. It seems unlikely that it would just keep building up for such a long period, but the key could be phosphorus: soil gradually loses phosphorus over time, and one way for plants to keep getting the phosphorus they need is to put more into the mycorrhizae that absorb it. Those same mycorrhizae also produce glomalin.


Glomalin: Hiding Place for a Third of the World’s Stored Soil Carbon, USDA Agricultural Research Service

Rillig, M., Wright, S., Nichols, K., Schmidt, W., & Torn, M. (2001). Large contribution of arbuscular mycorrhizal fungi to soil carbon pools in tropical forest soils Plant and Soil, 233 (2), 167-177 DOI: 10.1023/A:1010364221169

Wright, S.F., Starr, J.L., & Paltineanu, I.C. (1999) Changes in Aggregate Stability and Concentration of Glomalin during Tillage Management Transition Soil Science Society of America Journal 63, 1825-1829.

Written by Thomas Kluyver

20 June, 2010 at 10:10 pm

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Species area curves & neutral theory

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How many species are there here? It’s a beguilingly simple question, and a fundamental area of interest. A moment’s thought shows that the bigger here is, the more species there will be. So, if we start from a little patch of my lawn, and take successively larger heres until we’ve included the whole world, we can draw a ‘species area curve’. It generally looks a bit like this:

Graph of species vs sampling area (on log axes). Goes up steeply at local scales, then increases more gradually at regional scales, before turning steeper again at the largest scales.

It’s got three distinct parts: at local scales, the number of species increases sharply as you look at larger areas, then at regional scales it slows down, but at the very largest scales it picks up again. It’s easy to come up with possible explanations in words: at first, the number of species increases as you happen to ‘catch’ more species in your area, then it levels off because you’re mostly finding the same species again, and finally climbs as you encounter ‘exotic’ species that don’t live near your starting point. But can a mathematical model of species come up with the same sort of result?

Enter neutral theory. Laid out in a book by Stephen Hubbell, it tried to model a group of species by ignoring all the differences between them, imagining that every individual has the same chance of dying, the same chance of reproducing, and the same (small) chance of producing a new species. This is, to say the least, controversial, but remember that it’s a model: of course reality’s not like that, what’s interesting is how well such a simple model fits ecological patterns like the species area curve.

The very simplest version of neutral theory completely disregards where individuals are: when there’s a gap to be filled, any individual has the same chance of filling it. An extra development is the idea of a ‘metacommunity’, where individuals die and reproduce within one population, but occasionally disperse from one population to another

That sort of model can’t study the intricacies of species-area curves, though. Both of the studies referenced below used versions of neutral theory that do take account of where each individual is: ‘spatially explicit’ models, in the jargon.

Simple model represented by pie chart, metacommunity model by four connected pie charts, and spatial models by a grid of coloured squares.

James Rosindell and Stephen Cornell made a computer simulation, in which each individual occupied one square of a grid (it helps to imagine trees in a forest, rather than moving animals). When one dies, its square is most likely to be filled by the offspring of a nearby individual. This led to a species area curve with more or less the right shape, and by running the simulation many times, with different settings, they were able to get a decent fit to real-world data; it turned out that their original model had favoured the nearby individuals a bit too much when filling gaps, and they had to allow slightly more dispersal from farther away.

Computer simulations are unwieldy, though. For every change, the model must be run several times over, and some changes will make it slower: Rosindell and Cornell admit that at least one possibility was too “computationally expensive” to test. So James O’Dwyer and Jessica Green set out to make a mathematical model, a set of equations, based on probabilities, to act as a shortcut between the settings and the result.

They, too, start off with a grid, except that they allow more than one individual to share a square. The equations for this I think I can understand. Then they turn it into a different type of equation (a “moment generating function”), and then work out what happens if you make the squares of the grid infinitesimally small. At this point they use some maths from quantum field theory, the proportion of Greek letters goes up, and curly Z and downward-pointing-triangle put in appearances, so I won’t pretend to understand it at all. The result, however, is a curve with three parts, and realistic numbers for things like the speciation rate do give it the right shape.

So what does this tell us? Well, it seems that the pattern we see for the number of species in different sized areas can be explained without considering either biological factors, such as competition and adaptation, or geographical ones, such as the arrangement of landmasses. And it sets the bar for anyone studying the effect of such things: can they explain the pattern better than a neutral model does?


O’Dwyer, J., & Green, J. (2010). Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity Ecology Letters, 13 (1), 87-95 DOI: 10.1111/j.1461-0248.2009.01404.x
Rosindell, J., & Cornell, S. (2009). Species–area curves, neutral models, and long-distance dispersal Ecology, 90 (7), 1743-1750 DOI: 10.1890/08-0661.1

Written by Thomas Kluyver

6 June, 2010 at 11:00 pm

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How ivy hangs on

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German scientists studying ivy (Hedera helix) have shown that its roots stick to things in four distinct steps:

  1. Initial contact
  2. Roots grow onto the surface, and lignify (get tougher).
  3. Roots produce glue, which seems to react with the surface.
  4. Tiny root hairs anchor the root to any minute crevices in the surface.

There’s quite a bit more about how the root hairs manage the final step. Their walls are structured so that, as a root hair dies and dries out, it coils up, catching on any irregularities and pulling the root in to the surface. If you’ve got access to the paper, have a look at the electron micrographs (unfortunately I can’t put them up here).


English ivy’s climbing secrets revealed by scientists, BBC News, 28 May 2010

Melzer, B. et al. (2010) The attachment strategy of English ivy: a complex mechanism acting on several hierarchical levels, Interface, doi: 10.1098/​ rsif.2010.0140

Written by Thomas Kluyver

1 June, 2010 at 11:45 pm

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