New Paper on Mutualisms in Ecology Letters

Good news, everyone! My friend and collaborator Andy Shantz and I, along with our PhD. advisor Deron Burkepile, just published a new paper in Ecology Letters regarding the effects of nutrient enrichment (i.e. fertilizer, phosphorus runoff, sewage outfalls) on nutrient-sharing mutualisms.

Nutrient-sharing mutualisms occur when two species cooperate to exchange necessary nutrients between them. The most common example is plants and mycorrhizal fungi. These fungi live on or in the roots of plants and are very good at scavenging rare nutrients, such as nitrogen or phosphorus, from the soils. However, they are not very good at obtaining sugars, carbohydrates, and other carbon-based nutrients. Plants have the opposite problem. They fix sunlight and carbon dioxide into sugars and carbohydrates, but often cannot take up enough nitrogen from the soils. Mycorrhizae and plants share nutrients, with fungi receiving sugars in exchange for nitrogen, to the benefit of both parties. Corals and algae are another common example, wherein corals provide nitrogen to their photosynthetic algae partners in exchange for sugars.

Beneath the snow and dirt lies a vast network of roots and fungi that support this Ponderosa pine forest
Beneath the snow and dirt lies a vast network of roots and fungi that support this Ponderosa pine forest

The stability of these mutualisms hinges on the relative rarity of important nutrients, in this case nitrogen and phosphorus. There is some evidence that the plant, or more generally the photosynthesizing partner, regulates the amount of nutrients in the trade. Theory predicts that if limiting nutrients, like nitrogen, suddenly become non-limiting, then the mutualism should fall apart. After all, why should the plant continue to trade away valuable sugars when it no longer needs the nitrogen from the fungi?

Andy and I tested this prediction using a meta-analysis, which is a quantitative synthesis of published results. Sure enough, we found that nutrient-sharing mutualisms subject to nutrient enrichment showed signs of collapse. That is, when soils or water were fertilized with nitrogen or phosphorus, the heterotrophic partner (corals, fungi) suffered lower performance because the phototrophic partner (plants, algae) ceased trading sugars for nutrients.

What does this mean? Well, nutrient-sharing symbioses form the foundation of most ecosystems: most plants harbor mutualistic fungi, corals cannot exist with their algal symbionts, and lichens exist as a mutualism between fungi and algae. If these mutualisms weaken, then the foundation of most communities also weakens, although just how much remains to be seen.

Ten easy tips for better science writing

As you may be aware, reading science papers can be difficult. Language is verbose and cluttered, the vocabulary is full of jargon, and trying to make sense of it can make your head hurt. I feel that way and I spend my life reading research papers, so I can’t even imagine how non-scientists feel when they attempt to read primary literature. Actually, I can, because I remember being confused as hell reading papers as an undergraduate. This has led some reputable scientists to explain why most written science is difficult to follow. Of course, other equally reputable scientists had some alternative ideas. I actually agree with Dr. Gelman, author of the blog in the second link. It isn’t just most science writing that stinks (to use Dr. Pinker’s phrasing). Most writing stinks in general. Writing is hard. I’ve spent years honing my skills and they still aren’t great. Here are a few simple tips, in no particular order, I’ve picked up on how to write a clear and understandable research paper.

  1. Write in the active voice. As an undergraduate, I learned that science was to be written in the passive voice at all times (I did that on purpose). I’ve learned as a PhD. student that passive voice is boring and slow. Write actively wherever possible; it’s more engaging and interesting. For example, reword the first sentence of this paragraph: ‘As an undergraduate in the sciences, I learned to write in passive voice at all times’. Much better.
  2. First person is fineI also learned in undergrad never to use first person. This archaic rule has fallen completely out of style. Feel free to say ‘I did this’ or ‘We did that’. If you have co-authors, always use ‘we’ even if you did all the physical work. Often your co-authors (see advisors) had a stronger guiding influence than you suspect.
  3. Delete the word ‘the’. ‘The’ has to be one of the most overused words in writing. Read your sentence multiple times, both with and without ‘the’. See if it reads just as clearly without it, then delete it. This is a BIG one.
  4. Delete the words ‘of’ and ‘that’. Same as above. Don’t write ‘even if you did all of the physical work’. Instead, write ‘even if you did all the physical work’. Sounds better, simpler, more active. Instead of ‘a few tips that I’ve picked up’, try ‘a few tips I’ve picked up’.
  5. Use as few words as possible. I think this is good advice for giving public presentations, writing, and talking in general. Don’t write ‘small changes in temperature’ when ‘small temperature changes’ will do.
  6. Know what ‘As such’ really means. Please look this up, because this has to be pretty high on the list of misused phrases. ‘As such’ commonly appears as a transition, e.g. “Temperatures increase metabolic rates. As such, growth and respiration increase as well”. That is wrong. As such’ directly refers to the subject of the previous sentence, e.g. “I am a Phd. candidate. As such, I’ll be unemployed as soon as I graduate”. If you’re confused, replace ‘As such’ with the subject or description from the previous sentence, “As a PhD. candidate, I’ll be unemployed as soon as I graduate’. If it works, you’ve used ‘As such’ correctly. If not, try a different word. ‘Accordingly’ is good, but make sure your paper isn’t covered with ‘Accordingly’s.
  7. It’s OK to start sentences with ‘However’ and ‘Therefore’. Technically it isn’t (another rule I learned as an undergraduate). However, for impact, I prefer it. First, the technically correct way: “I agree with my advisor on most things. I find, however, that I strongly disagree with him on others.’ Second: “I agree with my advisor on most things. However, I strongly disagree with him on others”. I like the second one better, it gets the point across.
  8. Check your paragraphs. The first sentence of a paragraph is the intro. The last is the outro. You should be able to remove everything in between and get your major point across. The stuff in the middle is just details. Try it with the lead-in paragraph to this post. If you can’t remove the middle without sacrificing several important points, then you have too many main ideas in one paragraph.
  9. Following from #8, keep paragraphs short. Good god, please don’t write a page-long paragraph. Get your point across quickly.
  10. Most importantly, use short and simple sentences. My PhD. advisor is king of this, and it works very well. Write like Hemmingway. You don’t need to show off your incredible vocabulary or complex, Faulknerian trains of thought. Save that for the Archer fan fiction you keep in binders on your shelf. The stuff you want people to understand needs to be written clearly and concisely in simple language.

Honorable Mentions: COMMA SPLICING! Please cut down on commas. I reviewed a number of papers of both friends and anonymous authors and people like to put commas everywhere. Only put them where they belong. Also, write with a dog on your lap. A dog on the lap makes everything better.

Atala Season!

Over the past few weeks, Blue Atala caterpillars have been out in force. A single coontie plant in the park by my house could have 15 – 20 caterpillars. A week ago, the caterpillars all formed their chrysalids, so the coontie plants look like Christmas trees, evergreen shrubs with little red ornaments.

Atala chrysalids hanging from a coontie plant.
Atala chrysalids hanging from a coontie plant.

I can’t wait for the next week or so, when the park will be swarming with Atala butterflies.

What Do Research Grants Look Like? A Successful NSF DDIG Example

As you may or may not know, scientists don’t just get money for research given to them by federal or state governments, agencies, or universities. We have to write proposals and submit them for review whenever there is funding available. Only the best proposals get funded, and the odds of getting your proposal funded for any given opportunity is <10% (usually somewhere between 2 – 5% get funded, depending on the funding source and competition). I though I’d post my NSF Doctoral Dissertation Improvement Grant that was successfully funded (on the first try!) for anyone who wants to to see. This is in keeping with a new philosophy of science transparency, and there are some excellent lists of publicly available grant proposals. Hopefully, this helps you understand what goes into the beginnings of a research project, after all, no research is possible without funding, and getting funding isn’t easy. If you’re applying to one of these grants, hopefully you find this and can look it over to see what successful DDIG grants look like.

You can find it here.

Effects of Herbivory on Ecology of Treefall Gaps

Nate Lemoine, FIU PhD candidate and Smithsonian researcher, sprays treefall gaps within the Smithsonian Environmental Research Center with herbicide. Photos by D. Doublet
Nate Lemoine, FIU PhD candidate and Smithsonian researcher, sprays treefall gaps within the Smithsonian Environmental Research Center with herbicide. Photos by D. Doublet

Naturally-occurring treefall gaps are an important part of forest ecology, playing a prominent role in the regeneration of both pioneer and non-pioneer tree species. Nate Lemoine is setting out to understand how insect herbivory plays a role in the growth and health of plants at treefall gaps. By caging small plots within gaps, he is deterring deer and other animals from eating the plants. He is also using herbicide to deter insects from some plots to compare to controlled plots where only water is sprayed.

By Dejeanne Doublet

Caterpillar Food 101

By Dejeanne Doublet, intern Conducting research with insects means that you must take on the roles and duties of a caretaker.

This summer we worked with the caterpillar species Spodoptera exigua (beet armyworms) and their close relative Spodoptera frugiperda (fall armyworms). Both species were shipped to us in sheets of eggs containing roughly 1,000 caterpillars. Most caterpillars start out their lives as eggs on leaves. They usually don’t get to pick and choose their food at the beginning of their lives, and are usually forced to eat from the plant or tree where they hatched.

Some caterpillars will enter a wandering stage once they’re big enough. They may wander about from plant to plant, picking and choosing what they like best or they may stay put at one type of plant for the rest of their life.

  • The first step involves mixing the agar into boiling water until it is completely dissolved. Then, the temperature should to reduced to 85 degrees before adding in the remaining ingredients.

When you’re a caterpillar shipped to a lab with 999 other caterpillars, though, you don’t necessarily get to have an all-you-can-buffet of cuisines. Our lab doesn’t quite function like a Subway and you can’t always have it your way. However, we do make sure you’re eating all your nutrients and vitamins with a homemade concoction of Lepidoptera food.

The recipe consists of more than a dozen ingredients that are simply mixed into boiling water. Click here for the full recipe. Once the ingredients are mixed together, they form a thick substance that cools down to form a tapioca pudding-like concoction.

We poured the finished food goo into 8 oz. plastic containers, allowed it to cool, then placed small pieces of the sheets containing caterpillars eggs on top of the food. We then placed the containers in a 30 ºC chamber under lights that mimic a 16-hour day and 8-hour night cycle. The caterpillars usually begin to hatch a day from when they arrive as eggs. Within a few days, they’re growing and eating and growing and eating.

Spodoptera exigua at about a week old
Spodoptera exigua at about 10 days old. Photos by D. Doublet

 

Evidence for Climate Change in Miami

It turns out that Miami used to be a much more pleasant place to live, with a larger number of days below 70˚ C. Now it is hot nearly year round. This data is from a weather station at Miami International Airport and should be taken with a grain of salt, but the trend is clear.

A search for wasp nests

Good year for finding monarchs

Monarch caterpillars are not easy to come by. In the last five summers I’ve spent at the Smithsonian Environmental Research Center in Maryland, I’ve only come across several caterpillars per season. This year, our lab is full of monarch caterpillars with a count currently up to 13 caterpillars, three of which are forming their chrysalis shells and undergoing metamorphosis. 

With the use of a microscope, we can photograph monarch caterpillars up close and personal. The monarch caterpillar (Danaus plexippus) in these photos was one of the first caterpillars we caught this season and is now being raised in our lab at the Smithsonian Environmental Research Center in Edgewater, MD. Photo by Dejeanne Doublet
With the use of a microscope, we can photograph monarch caterpillars up close and personal. The monarch caterpillar (Danaus plexippus) in these photos was one of the first caterpillars we caught this season and is now being raised in our lab at the Smithsonian Environmental Research Center in Edgewater, MD. Photo by Dejeanne Doublet

 

 

 

 

 

 

Cheap and Effective Homemade Insect Clip Cages

Spent an afternoon putting these clip cages together.

I’ve been working with caterpillars, and I needed to find a way to keep the caterpillars on the leaf for a few days so I can come back and get them later. Clip cages are great for this. Bio-Quip sells them, but they are small (1″ inner diameter) and expensive ($40 for a pack of 10). Here’s a step-by-step guide of how to make your own clip cages. These cages are great for hobbyists wanting to rear insects, teachers who want to raise insects in a classroom, or researchers who need a way to do experiments (cheaply) with bigger insects.

1. Purchase the appropriate foam tube and supplies

Trampoline padding
Trampoline pole padding I bought online.

I used both trampoline pole padding (1.5″ inner diameter) and pool “super-noodles” (2″ inner diameter). Either one works well, is cheap ($3 – $5), and light (no more petri dishes that overload the leaf and cause sagging). A single tube can get about 15 full cages. Other than the tube, you only need window screening (cheap at home depot), contact cement ($4 per bottle), and long staples ($3 – $5 for 100). I like Powershot cable staples because they are wider than normal staples, but you need to pull the plastic end off to make them useable.

2. Chop up the tube

DSC_8340
Lots of little tube slices.

The tube should be cut into 2″ wide slices. You can use scissors, a razor blade, Exacto knife, or anything else. I used a chop saw to slice through six tubes in a matter of minutes. Also, the chop saw gave me a nice clean, straight cut. A band saw would work even better than a chop saw.

3. Glue the slices onto window screening

You can do this however you like. My preferred way is to lay the window screen on a table, coat one side of the foam slice with contact cement, and simply lay the slice onto the screen. Wait a few minutes for the cement to dry. This works incredibly well if you’re mass producing hundreds of clip cages like I was. Make sure you do this in a well-ventilated area. You’ll want to give the glue several days to dry and air out all of the fumes before putting insects inside.

Self-explanatoriness
Self-explanatoriness

4. Cut the foam slices out of the window screen

This is pretty self-explanatory.

5. Use staples to connect two slices

I use three staples per clip cage. Put the two halves together (window screen facing out on both sides), and use the staples to fasten them together.

6. Place on plant with insect. Enjoy

Here is the final product in action. Each cage should cost about a dollar, if that.

You'll have 15 of these things. Go nuts.
You’ll have 15 of these things. Go nuts.