Thomas' Plant-Related Blog

On plant science. Mostly.

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Salamander embryos go green

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I found out today that some salamander embryos have symbiotic algae. The algae use the salamander’s waste products as fertiliser, and the baby salamander (probably) benefits from the oxygen they produce by photosynthesising. That’s pretty cool, but it’s not really news, since the association was discovered about 120 years ago.

What is new is a finding by a Canadian & American group, that the algae actually get inside the salamander’s cells. That apparently makes it the first known case of a vertebrate having a symbiont inside its cells. People had suggested that vertebrate immune systems were too protective to let that happen. Salamanders’ immune systems aren’t that advanced by vertebrate standards, though, which might be why the symbiotic algae can get in. Or it might be because the immune systems of the embryos are still developing.

The researchers also found some hints that the algae can be passed down from the mother, but they’re not so confident about that.



Written by Thomas Kluyver

5 April, 2011 at 9:36 pm

50 Botany blogs (and plant plankton?)

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If you ever feel that you just can’t get your daily botany fix, a website about online learning has helpfully compiled a list of the 50 best botany blogs (including this one). Thanks, guys—not least for the reminder that I should keep on blogging.

As a scientist and pedant, I have to point out that plankton aren’t a plant species, though. Plankton is a general term for all sorts of small organisms that float in the water, including tiny animals and single celled algae. Are there any plants which could be called plankton? Perhaps the coconut, floating along until it finds a suitable place to grow, is roughly equivalent to the planktonic larvae of barnacles and the like. But I’m not sure that it counts if it’s dormant. Leave a comment if you’ve got a better idea!


Written by Thomas Kluyver

17 February, 2011 at 10:30 am

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Why trees have to leave home

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Tropical forests are a challenge for ecologists, because there are so many species. It’s not just a practical challenge to identify them, but a theoretical question of why they’re all there. Why don’t the better adapted ones win out, while others go extinct? Does every species really have its own ‘niche’—some set of conditions where it outcompetes everything else? Or are the different species much the same? (I’ve discussed neutral theory before)

A third idea is that trees can’t grow too close to their parents (or others of the same species), perhaps because pests and diseases spread between them. This is called the Janzen-Connell hypothesis, after the scientists who, independently, thought of it. If each species has to space itself out to escape pests, other species can grow in the gaps, without outcompeting each other. Some new evidence backs this up.

One study analysed where thousands of seedlings were growing, on an intensely studied plot on Barro Colorado Island, Panama. After five years, saplings with others of the same species nearby were less likely to have survived. Interestingly, the effect was apparently greater for rare species than for common ones; perhaps that helps to explain why they are rare.

Another experiment looked at seedlings grown in pots, with soil taken from under the same tree species, or another one. Seedlings grown in ‘home’ soil once again fared worse, suggesting that a disease or a pest in the soil could be the key.

Owen T. Lewis (2010) Ecology: Close relatives are bad news. Nature (News & Views) 466, 698–699

Ecology: Close relatives are bad news

Written by Thomas Kluyver

9 August, 2010 at 11:54 pm

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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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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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Digital flower art

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Composite image of a roseThese flower images are apparently produced by dissecting real flowers, and painstakingly making a 3D model in the computer. Image from Wired, and by Macoto Murayama.

Written by Thomas Kluyver

6 March, 2010 at 2:38 pm

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Assorted plant papers

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When finding the paper for the previous post, I ran into several more interesting planty papers. So, rather than just letting them go, here’s a brief summary of each.

  • A couple about the bacteria which live in the roots of the bean family, supplying them with nitrogen. One details a signal from the plant to the bacteria, in the form of a protein. What’s interesting is that it looks like the proteins that would normally kill bacteria, so evolution has changed a hostile interaction to a more friendly one. Another paper looks at the mechanism which lets the plant pass proteins to the bacteria.
  • Animals which live in trees have evolved to live longer than those on the ground. Flying animals were already known to live longer, but now we know it goes for tree-climbers too. The idea is that if you’re less likely to get eaten (or squashed, or drowned by flash floods…), it pays to take life in a more leisurely fashion, rather than living and breeding as fast as possible before something catches up with you. OK, so the link to plants is a bit strained, but it’s interesting all the same.
  • An interesting question for botanists is why seeds come in such different sizes (think about a bag of grass seed, say, versus a coconut). Someone’s done some modelling to suggest that it could be down to a trade-off: big seeds can survive in hostile environments, but small seeds have the the advantage in numbers.
  • I’ve previously mentioned the idea that RUBISCO, the key enzyme in photosynthesis, is already doing about as well as it could without a complete redesign. A new analysis supports that view.
  • Calculations show that forests are growing faster, and not just where they’re recovering from human damage.
  • Species diversity might depend on individual variation. Not sure I fully understand the idea, but it sounds a bit like the neutral theory of biodiversity. I might read this later.

Written by Thomas Kluyver

4 March, 2010 at 12:12 am

Posted in Uncategorized