If you are in sections 2,4,6,8,18 or Bio 105 You will be doing the reverse: Exercise 6 the week of February 11 th.

Transcription

1 Note: If you are in sections: 1,3,5,7,9,10,11,13,15,17 you will be doing Exercise 5: Population Growth the week of February 11 th and Exercise 6 during the week of February 18 th. If you are in sections 2,4,6,8,18 or Bio 105 You will be doing the reverse: Exercise 6 the week of February 11 th. THIS SHOULD INFORM YOU AS TO WHAT YOU WILL NEED TO READ IN ADVANCE FOR THE QUIZ ALL SECTIONS WILL HAVE AN IN-LAB REVIEW SESSION NEXT WEEK (11 TH -15 TH ) AT THE END OF THE LAB TO HELP YOU STUDY, WE WILL PUT A PRACTICE EXAM ONLINE BY SATURDAY

2 Exercise 5: Population Growth Oil Spills and Growth of Bacteria Introduction One of the most basic ecological questions is how fast a population grows. This is useful to know in all kinds of situations, from how diseases spread to saving endangered species. Understanding growth rates is important for everything from: basic scientific research, to determining bag limits on ducks or number of elk permits to issue to hunters, to dealing with problems associated with human overpopulation. Outline of This Lab Fossil fuels are one of the major power sources used around the world. Much of the world s oil comes from the Middle East, and thus, oil is frequently moved from one place to another on ships. Oil spills occur all too frequently and can cause major environmental damage. The effects of a spill can persist for years if the oil soaks into the mud, sand, and rocks near shore. Animals, such as birds and otters that get soaked in oil most often die. Through new technology, we have bioengineered oil-eating bacteria that show promise in getting rid of oil spills. Crude oil stores energy that can run our cars, but that energy can also be used by certain bacteria as a food source. If we could engineer an oil-eating bacterial species that grows quickly, perhaps we could spray these bacteria onto oil spills and they would literally eat the spill away. In this lab, you are a consultant to a company specializing in cleaning up oil spills. They just developed a new strain of bacteria for eating crude oil, and they want you to do some tests to tell them if this bacterial strain might be useful. To be useful and cost effective, these bacteria must eat 90% of an oil spill within 2 days. To get these bacteria to the spill you need to fly a plane over the spill and drop them from the air. A small plane can't hold many bacteria (relative to the size of a typical oil spill), so it's important that dropping just a small number of bacteria is enough to meet the 90%-gone-in-2-days goal. Your job is to decide if the strain of bacteria is good enough to do the job, and if not, whether they should invest time and money in making better bacteria or invest in bigger airplanes that can carry more bacteria to a spil1. You have a laboratory setup that is very useful for doing these experiments. You can put a bit of seawater covered with a thin layer of oil onto specially designed slides, add a fixed amount of bacteria to the slide, and then put this under a microscope. Your microscope is high enough power that you can see individual bacteria. You have an instrument connected to the microscope that will count the number of bacteria on the slide for you and make graphs of this number over time. Using this setup, you should be able to help figure out what to do with the bacteria.

3 The Lab 1. Open the Situation folder and find Oil Spills Use the OPEN command in the File menu. 2. You should see several windows laid out on the screen as follows: In the upper left is the Microscope Slide where we'll be doing our experiments. This slide is 1 mm on each side (you can stretch it out by dragging from the lower right corner), and is marked off in a grid pattern, with each grid square big enough to hold one bacterial cell. To the right are a graph and a table, which will show you how much bacteria and oil there is as the experiment progresses through time. In the bottom is the Control Panel, controls the experiments. Under the Microscope Slide is a window titled Experimental Parameters which we'll use later on. 3. The company has told you that it is economically feasible to add two bacterial cells per square millimeter, so we start out by adding only two cells to the slide (which, as you'll recall, is 1 mm 2 ). As the experiment runs, you should see bacteria moving around on the slide, eating the oil, and reproducing. When the oil runs out, the bacteria start dying from starvation. The first time through you should run the experiment stepwise. Each time you click the step button (red bar with green arrow) in the control panel you advance the experiment one-hour. With the first click, the oil is added to the slide (the spill). Continue stepping the simulation until hour seven. Normally, it would take several hours after a spill for a crew to get to the spill with the bacteria, so to simulate this lag we don't add the bacteria until 6 hours after the experiment starts. As you continue stepping hour by hour, you can watch the bacteria consume the oil and reproduce. Continue until 90% or more of the oil is gone. After you understand how the experiment works you can start the experiment by clicking the GO button (green arrow). Wait until all the action finishes and then stop the experiment by clicking STOP (red octagon) in the Control Panel. You can look at the Population Graph to get a better idea of how the bacteria population grows and shrinks. If the interesting part of this graph has moved off the edge, you can scroll backwards using the scroll bar at the bottom of the graph. The scale at the bottom of the graph is in hours. The computer also records the number of bacteria every 12 hours, which appears in the Population Table. 4. Write a short description of the growth of the bacteria, both from what you remember while watching the experiment and from looking at the graph. 5. Remember that the goal for whether this bacteria was successful was that it should eat 90% of the oil within 2 days (48 hours) of the spill. You can see the exact amount of oil left after each 12 hours in the Population Table. The initial amount of oil is about 2000 drops. Using only two bacteria per mm 2, are they successful at cleaning up the spill? If not, how far off are they? How many more hours did it take? 6. Since what happens is partially governed by chance, you should run the experiment at least a couple more times to see if your results from the first experiment were normal. To run the experiment again, reset it [click on RESET (brown button) on the Control Panel] and then start it again (GO). For each run, figure out the length of time it took until 90% of the oil was eaten. Then average these results.

4 As you saw, the bacteria are not eating fast enough to do the job. The company wants to know both how much more of this bacterial strain they would need to use per area of oil spill and, alternatively, how much better a new strain of bacteria would need to be to do the job with only two bacteria per mm 2. In order to find the answers, we need to figure out exactly how fast the bacteria are growing. We can calculate the growth rate from the bacterial counts in the Population Table, which shows the number of bacteria on the slide every 12 hours from the start to the end of the experiment. The growth rate of the bacteria is the number of new bacteria produced by each already existing bacterium in a given amount of time. Since we are measuring bacterial counts every 12 hours, it's easiest to calculate the bacterial growth rate per 12-hour period. A growth rate of 0.5 per 12 hours would mean that on average, each bacteria made one-half of a new bacterium in 12 hours (or to put it another way, one of every two bacteria reproduced in that 12-hour period). This growth rate then tells you how much the total population size of the bacteria went up over those 12 hours. If each bacterium is producing, on average, 0.5 new bacteria over the 12 hours, then the total population size will increase by 50%. We can also go backwards--if the population increased by 50% over the 12-hour period, then on average the bacteria must have produced 0.5 new bacteria, and so the growth rate must be Before calculating growth rates, try to predict when the bacterial growth rate of bacteria will be highest. Are the bacteria growing fastest when they are first added to the oil, when population size is highest, or somewhere in-between those two? Write down your prediction. 8. Calculate the growth rate of the bacteria. Remember, the growth rate is the number of new bacteria produced over the 12 hours by each individual bacterium which was already there. Calculate at least a couple growth rates near the beginning of the experiment, a couple when the bacteria are nearing their maximum population size, and one when the bacteria population is declining. Do the bacteria grow faster, slower, or at the same rate through the course of the experiment? Write down your answers, and a short explanation of why you think any changes in growth rate might be happening. 9. As above, you should repeat this experiment at least twice more to get average results (RESET the experiment and then run it again). To save time, when you repeat the experiment you can calculate growth rates just where they are going to be highest (as you determined in step 8). Now we have the information that we need to start making recommendations to your company. First of all, let's figure out how much extra bacteria they would need to add in order to be pretty sure of meeting the success criteria. They want to add two bacteria per square millimeter of ocean, as we've done in the experiments up until now, but if they needed to add just one or two extra bacteria, then maybe that would still be cost-effective. We can figure out the effect of adding extra bacteria from the growth rate. To use the growth rates you calculated, you would put them into a formula like the following: N t = N t rn t -12; where N t is the number of bacteria at time t, N t -12 is how many bacteria there were 12 hours before time t, and r is the growth rate. What this equation says, in words, is that the number of bacteria at time t is equal to the number 12 hours ago, plus the growth rate that you calculated above times the number 12 hours ago. You should be able to derive this formula from the formula you used to calculate the growth rate.

5 10. How will doubling the amount of bacteria we add initially (from 2 to 4) affect the time it takes them to eat 90% of the oil? It should take less time, but how much less? You should be able to calculate this from the growth rate that you figured out above. Write down how long you calculated it will take with the extra bacteria, along with the reasoning you used to make this calculation. If you are having trouble figuring this out, think about how long it took in the first experiment for the bacteria population to grow from 2 to 4 (which it no longer has to do, of course, when it starts at 4). Now we'll see if this prediction is correct. We can redo the experiments we did above with four bacteria added initially instead of two. Here's how to do that: 11. Find the Experimental Parameters window. The top item in this window shows how many bacteria to add to the slide at the beginning of the experiment. Right now it is set at 2. Replace the 2 with a 4, and then click on the CHANGE button at the bottom of the window. 12. Reset the model (RESET in the Control Panel), and run it again (GO). How long did it take for 90% of the oil to get eaten now? Repeat the experiment a couple times to make sure your results aren't just due to chance. Was this approximately what you predicted? 13. Now make a prediction for how long it will take to eat 90% of the oil if you double the starting number of bacteria again from 4 to 8. Write down this prediction. Then repeat steps using 8 bacteria. 14. Is this a very efficient way of reducing the time it takes to eat the oil? Remember that each time you double the number of initial bacteria, you are also doubling your company s cost and effort of using the bacteria. So do you get much benefit by paying for twice as much bacteria? Instead of using more bacteria, you can try to make a strain that is a bit more efficient at using the oil to grow. This would make the growth rate go up, because each of the bacteria wouldn't have to eat as much oil before reproducing. 15. Before we actually try increasing the efficiency of the bacteria, let's again try to predict what the result should be. If the bacteria are twice as efficient, this means they can reproduce twice as many times after eating a given number of oil drops, so that their growth rate should approximately double. From this, you should be able to make a rough calculation of how long it will now take for the bacteria to eat 90% of the oil, starting from just two bacteria. Write affect this prediction down, along with the reasoning you used to get to it. You will how not be able to make this calculation exactly, so you don't necessarily need to use the growth equation given above, but you should be able to get a pretty good rough answer just from thinking about what will happen if the bacteria reproduce twice as fast. The amount of energy that a bacterium gets from eating one drop of oil is shown as the second number in the Experimental Parameters window. Increasing this number will make the bacteria extract more energy from each drop of oil. This number is currently set to 2. Since we doubled the number of bacteria to see what effect that would have, let's also try doubling the efficiency. In order to make a fair comparison; we will first decrease the initial number of bacteria back to Reduce the starting number of bacteria back down to Increase the energy gained from a drop of oil from 2 to 4 by finding this item in the Experimental Parameters window, changing the 2 to a 4, and then clicking on the CHANGE button.

6 18. Reset the model and then run it. How long did it take for the bacteria to eat the oil this time? Was this what you predicted? Run the model a couple more times so that you can get an average result. 19. If both increasing the efficiency of the bacteria and using more bacteria cost about the same amount, would your recommendation be to stick with the bacteria they have now and try to use more of it, or to attempt to develop a more efficient bacteria? Why? Notes and Comments - What did we learn today? This lab should have given you a feel for exponential growth, and how even a small number of individuals can quickly grow into very many individuals. The speed at which the population grew depended on two things. The first was intrinsic growth rate. This is the bacteria's maximum reproduction rate--the speed at which they reproduced when they were completely surrounded by food. More generally, the intrinsic growth rate of a species describes how fast individuals can reproduce under ideal conditions. The only limits to growth of the population are then internal factors, such as how fast the individuals can eat, how fast they can make babies, and so on. Early on, in the experiments we did here, the bacteria were growing at a speed quite close to their intrinsic growth rate. Once the oil started to be eaten, the growth of the bacteria was limited by the amount of food available. Eventually, the bacteria ran out of food, and without food they died off. In many cases, this is the way nature works--some new source of food appears, creatures rush to take advantage of it, use it up, and then all die off or search for new food supplies. In many other situations, however, there is a steady supply of food instead of one burst. A given supply rate of food can support a certain number of individuals, and this number is called the carrying capacity of the environment. More generally, the carrying capacity is a measure of how large a population of the species can survive on a certain amount of resources. When you changed the energy bacteria gained from a drop of oil, you were changing both the intrinsic growth rate and the carrying capacity for the bacteria. You measured the increase in growth rate in the lab. The increase in carrying capacity wasn't directly shown, but you probably noticed that the peak bacteria population was higher when they were more efficient at eating oil. This increase in number of bacteria came about because the same amount of oil could support more bacteria, thus increasing the carrying capacity of the slide of oil. Both growth rate and the amount of resources it takes to support a given size population are routinely measured in many different situations. Almost anywhere else you look in ecology, evolutionary biology, and related fields, you'll see growth rates and carrying capacities being used. The observations that you made in this lab are similar to what we do in the real world all the time. For instance, people who breed new crops want to know how fast their new strains grow, and how much fertilizer is necessary to grow a certain amount of a crop. Conservation biologists worried about an endangered species are interested in how many individuals can be supported on the remaining habitat, and how quickly the remaining population could grow if more habitat was added. At the other end of the spectrum, people who study human demographics determine growth rates of human populations and use these growth rates to calculate how many people we'll have in the future. We re concerned whether the Earth's carrying capacity for humans is large enough to support these gigantic populations. That is, can the Earth support 10 billion people that we expect our global population to reach sometime this century?

7 Exercise 6: Predator-Prey Dynamics Introduction Predator-prey dynamics are thought to be a major reason that animals diverged to the major phyla that we see today starting in the Cambrian Explosion about 545 million years ago. When we look at fossils that date to this period, scientists notice two striking things. First, we see a massive radiation of different body plans that represent those we see today. Second, we see animals that have hard exoskeletons or outer shells for protection, and we did not see these structures in older, Precambrian species. Predators and prey are generally thought to be in an evolutionary arms race. Predators are always selecting for more elusive prey (remember, we saw many examples of prey adaptations in the Museum lab). But, as the fastest prey escape and produce the most offspring, predators, too need to be faster, and it is the fastest predators that survive and reproduce. Thus, you can see a continuing cycle of how predators need to be better at catching and eating prey, but prey get continually better at escaping. The arms race analogy comes from sociology; we were in an arms race with the former Soviet Union for quite some time each country kept making more nuclear weapons to compete with the other. A key to survival as far as prey species are concerned, then, is to eat, but avoid being eaten. This creates a classic tradeoff that has been well studied in ecology- the foraging-antipredator tradeoff. When prey hide from predators in refuge, food is often unavailable. But, when prey are feeding, they are often vulnerable to predation. Some birds, such as crows, have evolved a very interesting social way of attacking this problem. While birds are feeding, their heads are down, and they may not be able to see potential predators that are about to attack. Crows have sentinels that perch high and around the perimeter of the feeding group (but they can t feed) so that if a predator comes in, they can warn the rest of the birds in the group. Why not cheat and feed all the time? It turns out that the birds remember who takes turns as a sentinel and will ostracize individual birds who do not take their turn on watch! Even insects, such as water striders, will change their behaviors when predators are around. In the absence of predators, male water striders are pretty aggressive during the mating season, trying to mount any other water striders that are around (even other males!). However, in the presence of predators, they spend more time hiding and are much less aggressive. So, we can clearly see that predation can influence a prey species lifestyle and can prevent them from doing two things most important to survival, feeding and mating. The lab You will simulate predator prey dynamics in lab today. Each lab will split into two groups and one of the two TAs will each lead a group. Students will volunteer to receive special instructions from their TA as either Scientists or Predators. Another group of students will volunteer to be a prey species of their choice. As prey, you may feed only while in the box (marked by tape on the floor) and you are in refuge (safe) outside of the box. You feed by picking up food (candies) one at a time. After you pick up 10 candies, you may mate and produce one offspring by bouncing the ball off the wall. Then you can start feeding again; for every 10 candies eaten you may make one offspring.