Comic from Darwin Eats Cake.It’s … actually kinda plausible. But I think that, if Guillaume manages to overcome his vexation, he might also note that there’s probably some sort of marginal fitness benefit associated with landing a regular gig at Slate. ◼
No in-flight drinks on this trip. Photo by pheanix.◼
The nodule-y roots of a soybean plant. (Flickr: Pro-Soil AG Solutions)
Nitrogen is one of the elemental building blocks of life as we know it—it’s a basic component of amino acids, which are in turn the building blocks of proteins, which form the building blocks and moving parts of every living cell. The nitrogen interwoven in our tissues originated as part of the atmosphere we breathe, but the path from atmosphere to living flesh is far less direct than drawing a breath. Atmospheric nitrogen becomes useful to us animals only via an intimate relationship between a plant and bacterial growing in its roots.
The bacteria, called rhizobia, have the rare ability to “fix” free-floating nitrogen into biologically useable form. In return for this nitrogen source, the host plant allows the rhizobia to infect a specialized knob of root tissue, a root nodule, which it supplies with sugar for the benefit of its nitrogen-fixing guests. The plant uses the fixed nitrogen to make proteins for its own use, and anything that eats the plant afterwards benefits.
If all this sounds familiar, it’s because the interaction between plants and rhizobia is the focus of my developing postdoctoral research, and I’ve been writing about it as I’ve done more reading about it. Specifically, I’ve been interested in how plants might be able to make sure their root nodules house helpful bacteria rather than freeloaders, who enjoy the sugar supply inside the nodule without fixing nitrogen in return.
I’ve discussed a couple of different mathematical models that suggest some options. However, models are really just formal ways to follow through the implications of a particular idea, not necessarily descriptions of what actually transpires between a plant and the rhizobia inside its roots. So I thought it might make sense to step back and survey what we presently know about what goes on inside those root nodules.
A caribou in Denali National Park, Alaska. Photo by blmiers2.
Nasty stuff, regardless of where you drink it. Photo by Darby Rose.
Photo by joiseyshowaa.The September issue of the Carnival of Evolution is online now at The End of the Pier Show. Okay, it’s not as glamorous as the better known September issue, but it’s still the number one spot for a month’s worth of online writing about descent with modification and all its scientific, cultural, and political ramifications. A few highlights:
Tomatoes, one of many plants that play unwilling host to red spider mites. Photo by sylvar.Plant-eating insects must overcome some of the cleverest weaponry in the living world—from poisonous latex to sticky hairs—just to find a meal or a place to lay eggs. Many deal with their host plants’ toxic defenses by digesting them or sequestering them safely for personal use, but the red spider mite Tetranychus evansi simply turns them off.
Tetranychus evansi eats a wide range of plants, from tomatoes to potatoes. One female mite can eat enough to lay 50%-70% of her weight in eggs every day, and while that isn’t much on the scale of a single, miniscule red mite, it adds up quickly when colonies build into dense clusters on host plants, sucking them dry and covering them in webs of spun silk.
Most host plants respond to such an onslaught by ramping up production of chemicals that make them unpalatable to herbivores, or that interfere with the mites’ ability to digest plant tissue. However, a team of Dutch and Brazilian biologists recently found that T. evansi somehow short-circuits this response [$a].
The team, whose senior author is the Dutch biologist Arne Jannsen, discovered that mites raised on leaf tissue from tomato plants previously attacked by T. evansi survived longer and laid more eggs than mites raised on tissue from plants that had never been attacked. Analsyis of RNA from tomato leaves attacked by the mites revealed that they were producing fewer of the signalling proteins associated with responding to insect damage than leaves damaged by another, related mite species—and one protein was produced at lower rates than in undamaged leaves!
Mites, up close. Photo via AgroLink.In other words, the mites were not just preventing the host plant from boosting its defences in response to a mite attack—they were suppressing the defenses below what they would be without an immediate threat. Like a burglar cutting the power to a home security system, T. evansi can somehow prompt a hostile host to become more hospitable.
This raises another problem, however. With its defenses down, the host plant is also more hospitable to other insect herbivores, which could reduce the plant’s value to T. evansi, or even activate the alarms the mites have managed to suppress. A second study by the same team suggests that this may be part of the function of the webs T. evansi spins as it consumes its host.
In this second round of experiments, the group returned to the closely related mite Tetranychus urticae, which was used to stimulate plant defenses in the first study. Earlier work had found that some strains of T. urticae can tolerate or suppress host plant defenses [$a], though not nearly as effectively as T. evansi. That earlier work found that non-suppressing mite strains could benefit from living on the same plant as a suppressing strain, and the new study first demonstrated that this effect is even stronger when T. urticae shares a plant with T. evansi.
A whole lot of (presumably happy) mites. Photo via AgroLink.In contrast, T. evansi colonies fared worse in the presence of the non-suppressing mites, whether fed leaves that had already been attacked by T. urticae, or placed on a mite-free leaf of a plant with another leaf infested by the non-suppressing species. All else being equal, T. urticae benefits from the defense-suppressing activity of T. evansi, but reduces the value of the host plant to T. evansi.
Faced with this freeloading competitor, T. evansi apparently replaces the disabled plant defenses with webbing. The team found that even though T. urticae thrived when given evansi-chewed tomato leaves, the non-suppressing mites had difficulty colonizing leaves covered in T. evansi webs. Moreover, T. evansi introduced onto a plant with the non-suppressing mites spun more webbing than when introduced onto a mite-free plant; but they didn’t ramp up web-spinning when sharing a plant with another colony of their own species, suggesting that the mites can respond to competition by building up their defenses.
So not only does T. evansi possess the means to turn off its hosts’ biological security system, it erects its own defenses to protect the plant from one competitor that might try to take advantage of the situation. How, exactly, the mites interfere with plants’ defensive responses will be an interesting future line of study. I’d also be very interested to see whether other herbivorous insects—things larger than other mites, and not so easily put off by some silk security fencing—also preferentially attack plants disabled by T. evansi. ◼
References
Kant, M., Sabelis, M., Haring, M., & Schuurink, R. (2008). Intraspecific variation in a generalist herbivore accounts for differential induction and impact of host plant defences Proc. Royal Soc. B, 275 (1633), 443-52 DOI: 10.1098/rspb.2007.1277
Sarmento, R., Lemos, F., Dias, C., Kikuchi, W., Rodrigues, J., Pallini, A., Sabelis, M., & Janssen, A. (2011). A herbivorous mite down-regulates plant defence and produces web to exclude competitors. PLoS ONE, 6 (8) DOI: 10.1371/journal.pone.0023757
Sarmento, R., Lemos, F., Bleeker, P., Schuurink, R., Pallini, A., Oliveira, M., Lima, E., Kant, M., Sabelis, M., & Janssen, A. (2011). A herbivore that manipulates plant defence. Ecology Letters, 14 (3), 229-36 DOI: 10.1111/j.1461-0248.2010.01575.x
Beerquake. Photo by dongga BS.Boy, did I ever pick the right time to visit North Carolina. If only there were some sort of widely-available medium through which working geologists could explain what shook up the East Coast on Wednesday …
Finally, from a compilation of timelapse videos of plants, here’s climbing morning glory. Tropisms in action!
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Yes, I’ve actually kept busy enough this week to make it all the way to Friday without compiling the weekly linkfest. So, er, here’s the best thing not related to next-generation sequencing I did manage to see all week: Julia Child explaining the Miller-Urey experiment, then making her own “primordial soup.”
Video via Ferris Jabr. That original experiment turned out to be more successful than originally known. ◼
The future is in the cloud? Photo by Extra Medium.Biologists are about to have access to all the genetic data we could ever want. Unfortunately, once we have that data, we have to figure out where to put it—and some way to sift out the bits that answer the questions we want to answer.
That’s the first day of the NESCent workshop in next-generation sequencing methods in a nutshell.
Brian O’Connor, who gave the morning lectures, framed the immediate future of biology as a race between technologies for collecting genetic sequence data and technologies for storing and analyzing that data. Moore’s Law is that computer processor speed (really, the number of transistors packed into a single processor chip) doubles about every two years; Kryder’s Law is that computer storage capacity roughly quadruples in the same amount of time. But in the last few years, and for the foreseeable future, DNA sequence collection capacities are growing on the order of ten times every couple years.
In other words, there may very well come a day when the cost of storing and using a genome (or genomes!) belonging your favorite study organism will exceed the cost of obtaining those data.
O’Connor suggests that one major way to stave off the point where computing capacity limits data collection and analysis will be to use more “cloud” systems—remote servers and storage. Lots of institutions have their own servers and computing clusters. I’m already working with data sets too big to carry, much less process, on my laptop; I filter out the subset of sites I want on the server where the data is stored, and download (some) of that smaller data set for local work.
However, high-capacity computing facilities need a lot of lead time, and infrastructure investment, to scale up. That isn’t practical for individual projects. In such situations, and for researchers at institutions that don’t have their own high-capacity computing resources, commercial services may become a major alternative.
In the afternoon, we got started with one such alternative, Amazon EC2, or “elastic cloud computing.” Yes, that’s Amazon as in Amazon.com, the place where you buy used textbooks. It’s possible to rent processing capacity and storage from Amazon, and the services are provided in such a way that when you need more, you can just request it. “Instances” running on Amazon’s computing facilities can run Unix or Windows—you can interact with an instance via a remote desktop-type interface such as NoMachine’s NX system—and will run any program you’d care to have chew its way through your data.
All of this, of course, assumes you have the budget. It’s not clear to me how easy it’d be to estimate computing needs ahead of time for grant-writing purposes; but on the other hand, you can probably expect that whatever estimate you come up with will likely go that much further when you finally start working a year later. Over beer at the end of the day, Karen Cranston, the Informatics Project Manager for NESCent, told me that Amazon’s pricing is close enough to that of the high-capacity computing facility at Duke University that it’s often worthwhile to use EC2 for short-term, high-volume projects simply because it’s so quick and easy to bring new resources to bear.
As a not-yet faculty member, the cloud means I can plan to do genome-scale work even if I end up at an institution without the on-campus resources to build its own cluster. That’s potentially pretty liberating. ◼