All posts by Alun Salt

About Alun Salt

When he's not the web developer for AoB Blog, Alun Salt researches something that could be mistaken for the archaeology of science. His current research is about whether there's such a thing as scientific heritage and if there is how would you recognise it?

The most efficient trap isn’t always the most deadly trap

Pitchers plants are carnivorous. They catch small animals, usually insects to gain nutrients like Nitrogen. You’d expect that they’d evolve their traps to be as effective as possible. If an insect gets away, that’s one less meal, but that’s not what happens for Nepenthes rafflesiana

Nepenthes rafflesiana. Photo by i-saint/Flickr

Nepenthes rafflesiana. Photo by i-saint/Flickr

N. rafflesiana is a plant that grows in sunny parts of the forests of Borneo, Sumatra, and the Malaysian peninsular. It grows a couple of traps, though the upper traps lack the waxy crystals of the lower traps. Both traps have a peristome, a lip that is very slippery when it’s wet to encourage insects to fall in. But often is isn’t wet. In fact the change in humidity through the day means that it can be dry for eight hours or more. Dr Ulrike Bauer from Bristol decided to have a closer look at what was going on.

She and her team examined plants in Brunei, in the north of Borneo. At first they examined the traps of plants to see how they worked normally. They found the plants ate ants. They ate other things too. There were a few termites, along with some bees, beetles and spiders, but the bulk of food was ants in young pitchers.

Experimental set-up for Pitcher plants

Experimental set-up to test the effect of constant wetting on ant recruitment and trapping. On each N. rafflesiana plant, two pitchers were prepared in this way but only one pitcher per pair was connected to the water supply. Wetted and control pitchers were swapped halfway through the experiment. Image by Bauer et al. 2015.

Next she tried something simple but clever. She rigged up some pitchers so that they were moistened by a drip from a bottle. The aim was to find out if the peristome drying out during the day badly affected the plant’s ability to capture ants. Each ‘wet’ pitcher on a plant had a companion ambient pitcher rigged up in the same way – to counter the effect of the equipment. Half way through the experiment the pitchers were switched so the ambient pitchers were moistened and the wet pitchers left to dry in the ambient environment.

They found that wet traps captured more flies, so it seems that a wetter trap is more deadly. So do the traps drying out indicate a plant at the limit of it’s range? Maybe slowly becoming more deadly? Bauer thinks that something different is happening, the pitcher plants are using ant behaviour against the ants.

Ants search for nectar, which makes the pitchers effective traps. But if you kill an ant that visits you have just one ant. If that ant can go back home and bring her friends back then you have a party of ants coming to your trap. Bauer et al. found that traps were making batch kills, which suggests this is what’s happening. It’s a good explanation, but it bothered me. They also point out that mass kills are comparatively rare events. That’s fine if you have lots of traps, but a bigger gamble if you have just a few. However, Bauer et al. have an answer for that.

As I mentioned above N. rafflesiana doesn’t produce just one kind of trap. The lower traps have waxy crystals, so while the peristome isn’t always effective, the wax means the lower traps are always working. Young plants are close to the ground to begin with, obviously, so they start by building conservatively with always-on traps and then build more effective batch-kill traps when they can afford to play a longer game.

This is the kind of science I like. The basic idea is simple and easy to explain, but it still takes observation and some careful thought to work out what the observations are telling you. You can also tell that Bauer and her co-authors are confident of their findings, because the paper is written in a way that’s easy to understand. The fact they’ve found the most deadly trap isn’t always the most efficient trap is a bonus.

You can pick up the paper for free, it’s Open Access, at Proceedings of the Royal Society B.

Bauer U., Federle W., Seidel H., Grafe T.U. & Ioanou C.C. (2015). How to catch more prey with less effective traps: explaining the evolution of temporarily inactive traps in carnivorous pitcher plants, Proc. R. Soc. B, 282 (1801) DOI: http://dx.doi.org/10.1098/rspb.2014.2675

Deadly competition between parasites

There’s an interesting paper out in Nature Communications: Coinfection alters population dynamics of infectious disease. The paper is the study of Plantago lanceolata a common weed where I live in the UK. It’s found across Europe to India and Africa, and as an invasive plant in North America, China and Australia. It’s an example of why scientific names are so important, because I’d call it Plantain, but it’s nothing like the plantains that people eat as Musa.

P. lanceolata is host to a mildew, Podosphaera plantaginis. It looks like a white powder on the leaves of plants. In fact it’s burrowing roots into the leaf and growing spores to spread elsewhere above it. The parasite is not good for the plant, but it needs a live host to survive. Yet sometimes infections take a turn for the worse. What causes that?

The key is co-infection. Sometimes multiple strains of parasite infect a plant. When that happens things get much more complex. With a simple infection, the parasite only needs to overcome the plant. However, if a plant has multiple parasites, then they compete with each other. Normally a gentle approach would be enough for a parasite, but when there are multiple infections then a more aggressive attacker can pull resources from its competitors. At least that’s how you’d expect it to work.

To find out if it’s true Anna-Liisa Laine and her team based at the University of Helsinki carried out experiments and field surveys in the Åland Islands, southwest of Finland. This is part of a longer-term study on infection, so they had well-known plant populations to examine. In September (2012) they took a leaf from up to 10 plants per population and examined the DNA. They also infected leaves in the lab, and in garden plots.

I think the most striking result they got is in the graph below. The bars measure spore activity, and green and blue bars measure infections from single strains of mildew. The red is what you find when there’s a coinfection.

Coinfection increases spore activity

Singly inoculated plants shown in blue and green and co-inoculated plants in red. (a) Mean number of spores caught on microscope slides from singly inoculated (3=green and 10=blue) and co-inoculated (red) plants. (b) The proportion of live leaf traps that became infected. Error bars are based on s.e.m. Image by Susi et al.

Anna-Liisa Laine, who led the project said: “Here we find that coinfection by different strains of the same pathogen species completely change infection dynamics. These results are really just scraping the surface of how complex infection dynamics can be under coinfection. In our current work we’ve discovered that ribwort plantain populations in Finland contain hundreds of viruses. We’re now measuring how this within host disease community affects infection dynamics for a wide range of pathogen species.”

You can pick up the paper as an Open Access publication from Nature Communications.

Susi H., Barrès B., Vale P.F. & Laine A.L. (2015). Co-infection alters population dynamics of infectious disease., Nature Communications, DOI: http://dx.doi.org/10.1038/ncomms6975

Where did your cells come from?

If you look at your cells under a microscope, you’ll see nearly all of them have a nucleus, mitochondria and other equipment inside them. Eukaryotic cells, cells with a nucleus, are the basis of all complex life fungi, plants and us. The change from prokaryotic cell to complex cell is profoundly important to evolution of life, but how did it happen?

The favoured explanation has been that an archaeon swallowed a bacterium. The two developed a symbiotic relationship and evolved into eukaryotes. This explanation bothers me slightly because it needs the pair to do a lot of work fast, but I suppose if archaea are eating bacteria millions upon millions of times each day, then they’re making a lot of attempts.

David Baum, a University of Wisconsin-Madison professor of botany and evolutionary biologist, has proposed a new model for eukaryote evolution. His model is inside out and, to a non-biologist like me, it looks plausible.

Baum and his cousin Buzz Baum at UCL, argue that archaea developed protrusions called blebs, little arms if you like. These enabled the cells to interact with their environment better. Along the way they encountered bacteria and started to develop ways to exploit the energy of bacteria, while the bacteria were still outside the cell. The cells that did this better survived more often and reproduced until they had engulfed the bacterium.

Inside-out model for the evolution of eukaryotic cell organization. Model showing the stepwise evolution of eukaryotic cell organization from (A) an eocyte ancestor with a single bounding membrane and a glycoprotein rich cell wall (S-layer) interacting with epibiotic α-proteobacteria (proto-mitochondria). (B) We envision the eocyte cell forming protrusions, aided by protein-membrane interactions at the protrusion neck. These protrusions facilitated material exchange with proto-mitochondria. (C) Selection for a greater area of contact between the symbionts would have led to bleb enlargement and the eventual loss of the S-layer from the protrusions. (D) Blebs would have then been further stabilized by the development of a symmetric nuclear pore outer ring complex (Figure 2) and through the establishment of LINC complexes that, following the gradual loss of the S-layer, physically connected the original cell body (the nascent nuclear compartment) to the inner bleb membranes. (E) With the expansion of blebs to enclose the proto-mitochondria, a process that would have facilitated the acquisition of bacterial lipid biosynthesis machinery by the host, the site of cell growth would have progressively shifted to the cytoplasm, facilitated by the development of regulated traffic through the nuclear pore. At the same time, the spaces between blebs would have enabled the gradual maturation of proteins secreted into the environment via the perinuclear space through glycosylation and proteolytic cleavage. (F) Finally, bleb fusion would have connected cytoplasmic compartments and driven the formation of an intact plasma membrane, perhaps through a process akin to phagocytosis whereby one bleb enveloped the whole. This simple topological transition would have isolated the endoplasmic reticulum from the outside world, driven the full development of a system of vesicular trafficking, and established strict vertical transmission of mitochondria, leading to a cell with modern eukaryotic cell organization. Baum and Baum BMC Biology 2014 12:76   doi:10.1186/s12915-014-0076-2

Inside-out model for the evolution of eukaryotic cell organization. Model showing the stepwise evolution of eukaryotic cell organization from
(A) an eocyte ancestor with a single bounding membrane and a glycoprotein rich cell wall (S-layer) interacting with epibiotic α-proteobacteria (proto-mitochondria).
(B) We envision the eocyte cell forming protrusions, aided by protein-membrane interactions at the protrusion neck. These protrusions facilitated material exchange with proto-mitochondria.
(C) Selection for a greater area of contact between the symbionts would have led to bleb enlargement and the eventual loss of the S-layer from the protrusions.
(D) Blebs would have then been further stabilized by the development of a symmetric nuclear pore outer ring complex (Figure 2) and through the establishment of LINC complexes that, following the gradual loss of the S-layer, physically connected the original cell body (the nascent nuclear compartment) to the inner bleb membranes.
(E) With the expansion of blebs to enclose the proto-mitochondria, a process that would have facilitated the acquisition of bacterial lipid biosynthesis machinery by the host, the site of cell growth would have progressively shifted to the cytoplasm, facilitated by the development of regulated traffic through the nuclear pore. At the same time, the spaces between blebs would have enabled the gradual maturation of proteins secreted into the environment via the perinuclear space through glycosylation and proteolytic cleavage.
(F) Finally, bleb fusion would have connected cytoplasmic compartments and driven the formation of an intact plasma membrane, perhaps through a process akin to phagocytosis whereby one bleb enveloped the whole. This simple topological transition would have isolated the endoplasmic reticulum from the outside world, driven the full development of a system of vesicular trafficking, and established strict vertical transmission of mitochondria, leading to a cell with modern eukaryotic cell organization.
Baum and Baum BMC Biology 2014 12:76 doi:10.1186/s12915-014-0076-2

What I like is that there are steps to bringing the bacterium inside the cell, instead of Pow! it’s there and everything has to develop now. That’s probably an unfair over-simplication of the standard model, but the inside-out model makes sense as each step along the way seems to either use material it already has, or confer a small advantage for survival by itself.

While the event happened unseen billions of years ago, Baum and Baum have some ideas of how they can test the idea. Genetic data could help indicate that an inside out model is more likely than the standard model. Their model predicts that some parts of the cell developed in the opposite order to the standard model, though I’ll admit I don’t understand the details of how “COPII-like coatomers are derived from structural components of the nuclear pore, rather than the reverse”. However, I can see a list of clear predictions that Baum and Baum are making that someone can test, even if it’s clearly not me.

Fossil data would be nice, but highly unlikely, but there is another prediction. If prokaryotes can gain an advantage by developing blebs to interact with bacteria, then it should be possible to see some prokaryotes in the wild that look like the first eukaryote before it engulfed its partner.

Best of all, it’s a very positive paper. Baum and Baum aren’t simply saying everyone else is wrong, they’re proposing new topics to research and new things to study, new ways to look at problems. Even if it turns out they’re wrong, they could be wrong in a really interesting and helpful way.

You can pick up the paper through Open Access from BMC Biology.

Baum D.A. & Baum B. (2014). An inside-out origin for the eukaryotic cell, BMC Biology, 12 (1) 76. DOI: http://dx.doi.org/10.1186/s12915-014-0076-2

Do changes in water levels in wetlands give plants a backbone?

The usual rule whenever a headline asks a silly question is that answer is no, and that’s the same here because plants don’t have backs. However research by Hamann and Puijalon does show that emergence due to falling water levels can cause a biomechanical response.

The stresses for aquatic and terrestrial plants differ, because aquatic plants have the support of water to give them buoyancy. Hamann and Puijalon point out, if a plant can float then the chief stress it will have is tension as it is dragged by the local current. What it needs is an anchor and flexibility to cope with the forces on it. A terrestrial plant in contrast feels gravity much more. It has to support its own weight. Wind can put a plant in tension, but the force of gravity can compress some tissues. So the mechanical needs of a plant out of water are different to those in water.

Diagram of forces on aquatic and terrestrial plants

Schematic overview of the main forces (thick arrows) and stresses (thin arrows) acting on plants in aquatic and terrestrial environments. In the aquatic environment, buoyant plants withstand the drag forces resulting from current flow through tension (σ +). In the terrestrial environment, in addition to the force of gravity, self-supportive plants withstand drag forces induced by wind through bending (a combination of tension σ + and compression σ −). Diagram by Elena Hamann and Sara Puijalon.

This is a problem for a plant that is happily sat in water, until there’s a drought. When the water goes the plants are faced with a major change in environment. Can they change their physical structure to cope? Hamann and Puijalon expected that plants could increase their cross-sectional area and the proportion of strengthening tissue in their stems to increase strength. They also expected the stems to become stiffer.

They looked at a wide variety of species Berula erecta (Hudson) Coville, Hippuris vulgaris L., Juncus articulatus L., Lythrum salicaria L., Mentha aquatica L., Myosotis scorpioides L., Nuphar lutea L. and Sparganium emersum Rehmann. The plants were growing in wetlands along the Ain and the Rhône in eastern France. One set of plants was picked from submerged conditions and the other from close by in emergent conditions, to keep the population and growing conditions as similar as possible. They then tested the plants for strength and flexibility and examined them physically.
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Laughing gas no laughing matter for climate change

There’s an interesting article published in PLOS One that I like. It’s one of these things that’s very clever, but the basic idea is very simple.

Beech wood and leaves

The future of climate change might lie beneath the soil. Photo by Karl-Ludwig Poggemann / Flickr.

Temperatures are rising, and there’s plenty of research on how that might affect plants. In PLOS One this month Gschwendtner et al. investigate how rising temperatures affect the soil. In fact they look at the microbe community in it. Bacteria and archaea are part of the biological process of putting Nitrogen into usable form for plants. Knowing how they might react to climate change would be useful.

The experiment was very simple. At the Tuttlingen Research Station in southern Germany, Gschwendtner and her team took some beech seedlings, and the soil around them, growing on a northwest facing slope and replanted some of them on a southwest facing slope. They got more sunlight on the soil and so you effectively change the climate for those soil samples. Compare one with the other and you get to see what sort of changes warmer weather might have.

That sounds simple, but there are some obvious problems. If the geology of the new slope is radically different, maybe you’re just measuring the change in geology, not climate. So what they did was core the soil, to make sure the new sites were a close match for the old sites.

That’s fine, but there’s another problem. The moved seedlings will have moved. That might lead to stresses that the other seedlings didn’t have. If that’s the case you’re measuring stress not climate. So to get round that problem they also replanted the control sample in new locations on the northwest slope, so they had the same stresses too.

The target was to see how Nitrogen production in the soil was affected. Measuring the soil and sniffing for outgassing would be a pain, so they used a different technique. They tested the soil for specific genes. Sampling the soil and comparing the relative proportions and quantities of certain genes in the soil would give measure of the kind of activity going on. For example they looked for the genes nirK, nirS, cnor and nosZ as markers of denitrification. These are genes associated with microbes that take nitrates in the soil and convert them to gases. If there are more bacteria and archaea working on denitrification, then they will be more copies of these genes to find.

What they found is that these genes became much more common in soil samples from the seedlings moved to the sunnier position. They also followed up the experiment by simulating drought and flood. They found that the denitrifying microbes did better under those conditions.

This has a double blow for plants. The first is that the plants are competing with these microbes for nitrogen. We think of plants living off carbon dioxide and water, but building proteins needs nitrogen too. The second blow is that the nitrogen is lost from the soil when the microbes emit it as nitrous oxide N2O. It’s known as laughing gas, but it’s also a greenhouse gas, adding to the climate problems the plants are already facing.

I think what appeals to me about the paper is the clever way they’ve looked at denitrification. If I wanted to measure change of nitrogen in a soil, I’d try directly measuring the nitrogen. Looking for DNA markers is simpler, and it also gives an idea of what might be driving that change. I also like the simplicity of the idea let’s move seedlings from here to there, and the fact that the control was replanted too. With hindsight it’s easy to say that should be done, but I bet that wouldn’t have occurred to me until the experiment was near its end.

As it’s in PLOS One you can pick it up now as an Open Access paper.

Gschwendtner S., Tejedor J., Bimueller C., Dannenmann M., Kögel Knabner I. & Schloter M. (2014). Climate Change Induces Shifts in Abundance and Activity Pattern of Bacteria and Archaea Catalyzing Major Transformation Steps in Nitrogen Turnover in a Soil from a Mid-European Beech Forest, PLoS ONE, 9 (12) e114278. DOI: http://dx.doi.org/10.1371/journal.pone.0114278

Inflorescences take centre stage

Inflorescences issue cover Annals of Botany has a new special issue in Free Access: Inflorescences. It’s a useful reminder to me of another area of Botany I need to read more about.

For a start, I think I’ve said elsewhere that inflorescences are the structures where there are multiple flowers on a plant and not just a single flower. In a clumsy way this might be true but it also misses the point of an inflorescence. It’s not simply that there are multiple flowers, but also that those flowers work with each other as unit. They’re not just a collection of individuals.

If you approach inflorescences from this point of view, their structure becomes a bit of a puzzle. Why the diversity? But also, can you classify them sensibly and, if you can, what is the basis of that? Do different structures correspond with different functions?

Lawrence Harder and Przemyslaw Prusinkiewicz describe the interplay between inflorescence development and function as the crucible of architectural diversity. It highlights the importance of linking structures and function. In terms of tracing plant relationships, structure is useful but it’s also worth looking at what the structure does. A similar structure could have a very different result if the phenology, the timing of the flowering, changes.

Time is key factor that is highlighted by Harder and Prusinkiewicz. Looking at a display, it’s easy to think of it as an organisation in space, but they also make a point that inflorescences are dynamic. They change with time, and how they change with time has consequences for their function.

As far as plant reproduction goes, it’s easy to focus on the success of flowers, but Harder and Prusinkiewicz argue that what you have is part of a modular system, and that to understand it you have to look at the system as a whole, instead of modules in isolation. Most angiosperms use inflorescences so it’s clearly a powerful tool for a plant. Looking at them as a unit and not just parts can put plant reproduction into a new context.

Harder L.D. & Prusinkiewicz P. (2012). The interplay between inflorescence development and function as the crucible of architectural diversity, Annals of Botany, 112 (8) 1477-1493. DOI: http://dx.doi.org/10.1093/aob/mcs252

The Guardian tackles the ethics of rewilding

The Guardian posted an interesting article yesterday from Tori Herridge: Mammoths are a huge part of my life. But cloning them is wrong.

Mammoth

Mammoth of BC by Tyler Ingram / Flickr.

I’ll concede that a mammoth is not a plant, but part of what I found interesting is that Herridge points out that mammoths didn’t exist in isolation. She tackles the idea that mammoths could somehow be part of a plan to restore the arctic steppes, but she makes an important point:

There’s a reason the terms “de-extinction” and “rewilding” are so powerful and that’s because they imply a return to a time, a state of grace, a place that was somehow unspoiled. Cloning a mammoth offers us the hope of undoing the excesses of humanity, bringing back the creatures whose extinction we helped bring about.

I think the idea of turning back the clock, to a time when things are better, is a powerful image. However it isn’t practical. Herridge points out that the mammoth was part of a wider ecosystem of arctic steppe, and it’s not certain that the plants will naturally appear if you dump a load of mammoths in Siberia.

It’s not even purely about the plants. Looking this up I saw there was a lot about remediation in the Root Biology special issue of Annals of Botany (now free access). In particular, Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that ‘everything is not everywhere’ say Rout and Callaway. They’re talking about microbes in the context of invasive species, but I wonder what ten thousand years of change has done to the soil of the arctic.

We don’t have the plants, we may not have the right soils. We are going through a big extinction event. I’d love to see a mammoth, but sadly when you look at the social problems a mammoth would have, as well as the many conservation efforts competing for limited funding, I think Tori Herridge is right, and that she does a good job of explaining all the problems.

Microgravity and chromosome damage

The Karyological Observations of Krikorian and O’Connor look at plant material from flights STS-2 and STS-3 of the Space Shuttle.

STS-2, among other things, carried a payload of Helianthus annuus, sunflowers. STS-2 was cut short from five days to two when a fuel cell for producing electricity and processing water failed. Despite this the plants had some time to grow, in a couple of cases with roots protruding from the soil. Krikorian and O’Connor say: “The soil environment of the roots in the HEFLEX-type modules was not particularly well suited to recovery of roots tips for karyological examination.” In plain English it sounds like it was extremely difficult, and they go on in the paper to explain some of the problems they had.

The key result was that when they looked at the cells, they found only around 2% were in division. The same plant in a lab would be expected to be ten times more active. They also found some plants had aneuploidy. Usually chromosomes come in pairs, (though polyploidy is common in plants too). In this case one plant was missing a partner for chromosome 6. The same was true in another plant from the sample. Given these results, similar tests followed on the STS-3 material.

Again with the oats, it was found that only a 2% of cells were in division, again about ten times less than anticipated from the lab. There was also chromosome damage. The mung beans too were found to have low counts for division, though less obvious signs of damage to the chromosomes.

It seems something was affecting the plants, but in their conclusions Krikorian and O’Connor were wary of saying exactly what. The obvious suspect is microgravity, but they also left open the possibility that it was the effect of launch and/or re-entry that was the problem. It’s this referring back to the control that marks out the value of the research on STS-3. It wasn’t simply that material was put into orbit, it was also that the same equipment was run on the ground to act as a control. If gravity is the variable you’re changing then it’s essential to get as much of the rest of the control experiment to run as closely to the orbital experiment as possible.

Like some of the other papers in this supplement, Karyological Observations has been cited this year in a paper Seed-to-Seed-to-Seed Growth and Development of Arabidopsis in Microgravity published October 2014 in Astrobiology. Link et al. also cite Kuang et al from 1996, Musgrave et al from 1998 and Kuang et al from 2000. In some ways it might be surprising that work from thirty years ago is still getting cited, but that’s how science works.

Currently NASA does plant science in orbit on the International Space Station, but this latest platform was built with the shuttle and the aging Russian Soyuz craft. In a similar way current plant research is built on the prior work of earlier scientists. Fortunately you don’t have to wait thirty years to see most research in Annals of Botany. If your library doesn’t have access to the journal, papers become free access a year after paper publication.

Space Shuttle landing

STS-3 lands at White Sands. Photo: NASA.

You can read more posts on papers from our spaceflight supplement by clicking the STS-3 tag.

Today’s Papers

Krikorian A.D. & O’Connor S.A. Karyological Observations, Annals of Botany, 54 (supp3) 49-63. DOI:

KUANG A. (1996). Cytochemical Localization of Reserves during Seed Development inArabidopsis thalianaunder Spaceflight Conditions, Annals of Botany, 78 (3) 343-351. DOI: http://dx.doi.org/10.1006/anbo.1996.0129

Kuang A. (2000). Influence of Microgravity on Ultrastructure and Storage Reserves in Seeds of Brassica rapa L., Annals of Botany, 85 (6) 851-859. DOI: http://dx.doi.org/10.1006/anbo.2000.1153

Link B.M. & Bratislav Stankovic (2014). Seed-to-Seed-to-Seed Growth and Development of Arabidopsis in Microgravity , Astrobiology, 14 (10) 866-875. DOI: http://dx.doi.org/10.1089/ast.2014.1184

MUSGRAVE M. (1998). Changes inArabidopsisLeaf Ultrastructure, Chlorophyll and Carbohydrate Content During Spaceflight Depend on Ventilation, Annals of Botany, 81 (4) 503-512. DOI: http://dx.doi.org/10.1006/anbo.1998.0585