Latest Activities

Your microbiology experiments

posted Nov 13, 2017, 4:54 AM by Beth Orcutt

Greetings, microbe adopters! I hope that you all have recovered from the big storm from two weeks ago and are now getting ready for some of the first winter snow. We’ve been having an interesting time readjusting to the cold here after so many weeks in the warm sun in the Atlantic Ocean and near Barbados.


Speaking of warm places, how did your experiment go with heating up some microbial yeast cells to examine the gases that they produce as they grow? It seems that maybe our experimental design has not been perfected yet, since your experimental notes indicate that the balloons did not inflate very much, although you did notice that the small bit of gas smelled like bread and muffins. As a scientist studying microbes in the environment, sometimes this happens – an experiment does not go as planned, so you have to spend a little bit of time troubleshooting to figure out what went wrong and then try again. Having the patience and confidence to overcome these setbacks are key ingredients for being a successful scientist!


Some of your troubleshooting suggestions included trying to tighten the tape seal between the balloon and the glass vial, since some gas may have escaped. Good idea! Temperature regulation may have also been issue, and maybe the experiment could be tried again with a different oven. Another thought to consider is that maybe the amount of yeast we used was too small to make enough gas to fill the balloon. Perhaps if we scaled up the experiment in a larger glass container with more yeast and sugar, but kept the same balloon size, we would see more gas production.


This issue of scale is really important for scientists studying life below the seafloor, like we were doing on the cruise we just went on. Sometimes there aren’t a lot of microbes per volume of material – like, maybe only 100 cells per teaspoon of rock or sediment instead of millions of cells, like we would expect to find in samples from close to shore – so we have to come up with new ways to try to concentrate the cells, or the gases that they produce, to increase the signal. This requires a lot of creativity, and patience with troubleshooting!


Thankfully, the second experiment to grow colonies of environmental microbes in Petri dishes seemed to be much more successful! We were really excited to see the time lapse photographs of your microbes.

Violet’s plate had many hundreds of red colonies of microbes.

Hope got to see some interesting interactions between microbe colonies and some mold that also grew in the plate.


Some of the scientists on our cruise were using similar methods to try to isolate and grow microbial bacteria, and also fungus/mold, from our deep-sea environments. Instead of using the solution that you used to make your Petri dish plates, the scientists used different solutions to account for the amount of salt in the ocean and also the different food needs of the microbes that they were trying to grow.


Now we are all back in the lab, starting to work on our samples. Thank you so much for participating in this Adopt A Microbe project with us – we hope that you had fun learning about microbes in the deep ocean. We look forward to a chance to meet you in person to show you our lab in real life!

no power, no problem

posted Nov 6, 2017, 3:25 PM by Beth Orcutt

Greetings, microbe adopters! The Adopt A Microbe team members have safely returned from sea and are re-adjusting to life at home. For those of us in Maine, that might be returning to a house without power, after last week's big storm. Since some of you may also be without power, we've decided to extend last week's activity for another week, so you have plenty of time to send us your updates. We look forward to hearing from you!

The final week - Microbe Farts and Growing Microbes

posted Oct 31, 2017, 3:40 PM by Beth Orcutt

Greetings, microbe adopters! We are excited to share this week’s activities with you, as we think they are some of the most fun. You will be doing two different experiments this week to learn about how to grow microbes and figure out what they are doing in the environment. The first experiment is all about “farting” microbes, and how microbes process chemicals in the environment. Before you turn up your nose, have no fear – while some of the following information will explain to you the science of gas production, there is no human farting required in making this activity work!! In the second experiment, you will grow some microbes using techniques similar to what scientists use to grow microbes from the environment, in a little more advanced way than the Winogradsky columns you built early on in the project.

First, a little background - When some microbes eat sugars and other organic material, they generate different gases as waste products. These gases can include carbon dioxide, hydrogen, methane, gaseous alcohols like ethanol and methanol, hydrogen sulfide and other sulfurous compounds (which smell like rotten eggs), and gaseous fatty acids like acetic acid (what vinegar smells like), formic acid (the stuff that makes ant bites sting), and butyric acid (really stinky stuff that kind of smells like throw-up – yuck!).  Did you smell any of these odors coming from your Winogradksy columns when you made your observations last week?

In humans and other animals, the gases that microbes living in our gut make from eating up sugars contribute to the gas released in flatulence (a.k.a. farts, although the majority of fart gas is actually swallowed air, or, in the case of soda drinkers, the swallowed fizzy carbon dioxide bubbles). Contrary to popular belief, the methane gas in farts is odorless! Most of the smelliness of farts actually comes from the gaseous sulfur compounds that are generated from food digestion. Some foods, like cauliflower, eggs and meat have more sulfur compounds in them, so they lead to stinkier farts.

What does this have to do with the microbes from the deep dark ocean that you adopted?!? Well, in a similar style to the microbes in your guts, some microbes living in the deep dark ocean also generate gas. For instance, the adopted microbes Methanocaldococcus generate methane gas, and Archaeoglobus and Desulforudis make stinky hydrogen sulfide gas from the sulfate that they eat. You can think of this gas production as “microbe farts”! 

During ocean research expeditions, some scientists deploy special gas samplers down into the ocean crust to analyze which kinds of gas are found down there, and how concentrated the gases are. While a lot of the gases in the rocky crust are produced during the hydrothermal interaction of the fluids and the rocks, some of the gases might also come from fartin’ microbes! By analyzing those gas samples, the scientists get a better idea of which types of microbes are living down in the rocks by the types of gases that are generated. It’s kind of similar to someone guessing what you ate for dinner by the smell of your farts! If you’d like to watch a video of some scientist friends of mine collecting samples from the bottom of the ocean, check this one out:

Looking for Life (IODP Expedition 337)

As promised, though, the first experiment isn’t about your farts. Instead, you will use some hardy yeast microbes to examine gas production. Yeast – the stuff that you need for making bread and other fermented products – are actually microscopic eukaryotes. They are different from the microbes you have adopted, which are all bacteria or archaea, because they actually have a cell nucleus like animal and plant cells.  Because of their tiny size, you can consider them to be honorary “microbes” for Experiment 1. 

For the second experiment, imagine your mouth for a moment (or, take a good look at your mouth in a mirror!) – that nice warm and wet environment that sometimes gets dosed with sugar is a happy place for microbes to grow. When they get out of control, these microbes can rot your teeth and form cavities.

 Now imagine the rocks in the warm water under the seafloor, full of hungry microbes…can you connect the similarities? Of course, rocks under the seafloor are made of different substances than your teeth, and the microbes are getting energy in different ways in both places, but the principle of a surface-associated lifestyle is similar.

For the second experiment, you are going to grow some rock eating microbes, using the same kind of techniques that doctor's use to study microbes that are growing on your teeth. In this technique, you will inoculate some sterile media (also known as food) in a Petri dish with microbes that you swab off of the surface of a rock from the environment (or you can dip it into your Winogradsky column!).


Note: an educator version of these activities is available on the web here.


Materials required:

·      Microbe Farts Activity:

o   measuring spoons (1/8 teaspoon, 1 teaspoon)

o   dry active yeast (you can find this in the baking section of the grocery store)

o   sugar

o   Glass vials with screw caps:

§  Available from Wards Geology: $14.20 for 12 pack, 8 ml size, part 6356502

o   balloons

o   A few rubber bands

o   Some electrical tape

o   Some water

o   A marker

o   An oven or hot plate set to 120-160 degrees Fahrenheit

o   a baking dish

o   optional: digital camera

·      Growing Microbes Activity

o   Surface Microbe Experimenter Kit (with package of sterile Petri dishes, package of custom Easygel media, a package of sterile cotton swabs, and directions)


o   Some wet rocks from the outdoors, stored in a plastic bag, as the source for inoculating the experiments.

§ Alternative: you can also use the material in the Winogradsky columns you set up, if you still have them.

o   bleach


Experiment 1:

1.     In the glass vials provided, mix 1/8 teaspoon of sugar with 2 teaspoons of water, then add 1/8 teaspoon of dry yeast and mix well.

2.     Carefully attach a balloon to the top of the glass vial, trying to keep the balloon as air-free as possible. Use a rubber band to hold the balloon tightly in place, then wrap some electrical tape around the base of the balloon to attach it tightly to the bottle. This will keep any gas from leaking out. 

3.     Place your balloon-covered vial into the baking dish and place it all in the oven or on hot plate. By careful that the balloon will not touch the heating element in the oven.

4.     After 1 hour, check on the experiments: Any changes in the balloon or in the yeast mixture?




5.     Gently shake up the bottle to remix the yeast, and put back on the hot plate. After 2 hours, check on balloons again. How do the experiments compare to the 1 hour condition?




6.     Carefully remove the balloon from the vessel and gently squish out some of the gas trapped inside to do a smell test (if you are up for it, have some take your picture while you are doing this!). What does the gas smells like?




7.     What kind of gases do you think that the yeast were making?




8.     How do you think a scientist would collect samples of gas from microbes at the bottom of the ocean?




Experiment 2:

Note: this activity takes a day or so to complete. IMPORTANT NOTE: The experiments outlined below should be safe to perform with adult supervision, but participation in the activity is completely voluntary and done at your own risk. Please read and follow the directions carefully and avoid contact with anything that grows inside the Petri dishes experiment, just to be on the safe side. Try not to open up the Petri dish once the microbes have started to grow in there – some of them may be harmful.  When you are done with the experiment, please have an adult carefully place a drop or two of bleach (or some vinegar) into the Petri dish to disinfect the plate for a few minutes, and then it can be placed into the trash.

1.     If you have a chance to go out into the environment to collect a wet rock, you can do that. Alternatively, you can carefully open up the plastic wrap on your Winogradsky column to access the yummy microbes growing in there.


2.     Rub the cotton swab over the rock surface or into the Winogradsky column, then carefully open up one of the Easygel bottles and stir the swab around in the solution for a few seconds.


3.     Carefully open up one of the Petri dishes and pour the Easygel solution into it, then close the lid as quickly as possible (to prevent airborne microbes and particles from landing on their sample) and keep the dish level (to prevent it from spilling). 


4.     Put a few pieces of tape around the closed Petri dish to keep the lid from falling off. In less than an hour, the gel solution should solidify.


5.     Write down your name on the Petri dish. It is a good idea to write on the outside edge of the dish lid, so that you can have a clear view of the middle of the plate. Store the plates at room temperature away from direct sunlight.


6.     Check on the plates over the next 3 days, and if you like, go ahead and take a picture if you see something that looks interesting. Record if and when any little red dots appear in the gel. Red dots are colonies of microbes that came from the sample and are growing on the media in the Petri dish. How many colonies appeared?



7.     Do you see spots that look like mold? If yes, do you think that these came from the sample, or from the air?




8.     What would be some of the challenges of applying this growth technique to microbes from rocks from the bottom of the ocean?



We hope that you have fun with these experiments, and we look forward to hearing from you about what you found.

Your week 5 Winogradsky columns

posted Oct 31, 2017, 8:01 AM by Beth Orcutt

Greetings, microbe adopters, and happy Halloween from the Research Vessel Atlantis. We are cruising through the ocean on our way back to port, and cleaning up the labs and finishing our reports before we don our Halloween costumes.


Thanks for sending in your observations from your Winogradsky columns as you learned about environmental microbiology! It sounds like you all have some stinky microbes growing! Before we get to the pictures and your observations, though, let’s review the answers to the math questions from last week.


The first question asked you to think about how many microbes are “buried alive” in the muddy sediment at the bottom of the ocean, and how long an imaginary string of these microbes would be if you lined them up side by side. Our best estimates are that there are 10 to the power of 29 (or, 1 with 29 zeroes behind it, which can also be written as 10^29) microbes living below the seafloor in sediment. If we assume that each microbe is 1 micrometer in diameter (which is 0.000001 or 10^-6 meters), then a string of 10^29 microbes would be 10^29 micrometers in length, or 10^23 meters. Would this string of microbes reach from the Earth to the Sun? Considering that the distance to the sun is 1.5 x 10^11 meters, then yes, this string of microbes would definitely reach from the Earth to the Sun. Interesting to think about.


The second question asked you to calculate how many microbes live in the dark ocean waters above the seafloor, if you assume that there are 50,000 microbes per teaspoon of seawater and that there are 2 x 10^23 teaspoons (200,000,000,000,000,000,000,000!) of water in the ocean. That would equal 10^28 microbes (10,000,000,000,000,000,000,000,000,000!). And that is only a tenth of the microbes that we think live in the sediment below the seafloor.


The final question asked you to calculate how many rolls of toilet paper, at a minimum, are required for a 30-day expedition on the RV Atlantis with 52 people on board, if each person needs about 50 sheets of toilet paper per day and every roll of toilet paper has about 500 sheets. At a minimum, the ship needs to carry 156 rolls of toilet paper so everyone is happy.


Alright, so how about your Winogradsky columns? Have you seen the development of any colored bands or noticed any other features that might indicate that you’ve got some microbes growing?

This before and after shot of the Winogradsky columns that Olivia and Violet from Lamoine set up show some interesting developments. Olivia’s column (on the left side), which has sandier sediment, shows the development of some reddish brown layers. What does that remind you of? It reminds me of rust. I’m guessing that some aerobic iron oxidizing bacteria that use reduced iron and oxygen, like Marinobacter and Mariprofundus do in the deep ocean, might be growing inside this column. Violet’s column on the right, which was much darker and more organic rich, has developed some green layers and is very stinky – indicating that some sulfur cycling microbes have started to grow.

Hope from Orland also has some green layers appearing in her Winogradsky column and smells some stinky rotten egg smell – definitely some sulfur cycling microbes growing in there!


Congratulations on growing your own microbial zoo! If you let your Winogradsky column keep cooking, these layers will continue to develop. You can even use them as source material for this week’s activity, which will be posted very soon.

Your week 4 seafloor features and microbe habitats

posted Oct 24, 2017, 10:34 AM by Beth Orcutt

Greetings microbe adopters! We hope that you enjoyed learning about density and buoyancy and how that effects water movement and the way that we adjust weight on the ROV Jason to get to the seafloor and back. You also experimented with how water moves through different materials like sand and soil and reacts with different types of rocks, and then used this information to think about what materials would make ideal substrates for your microbes. What did you come up with?


Hope from Orland imagined her adopted microbe Marinobacter living within cracks and spaces within rocks. She also thinks that sand would be a good substrate for microbes to live in.


Violet from Lamoine imagined her adopted microbe Acrobacter living near hydrothermal vents on the seafloor, where basalt and pyrite rocks can be found. After doing her experiment of how water moves through sand and soil, she suggests that soil would be a good environment for microbes because soils also have rocks that react and provide food for microbes to eat.

  In truth, microbes can be found in all of these environments, and have developed strategies to make the most out of the conditions they are in. Sandy sediment has the advantage of getting flushed with water more quickly than clay-rich muddy sediment, so that is helpful for flushing out waste and resupplying nutrients, but not so great for keeping carbon around. Sediment has more carbon, but the replenishment of nutrients is much slower.

Speaking of carbon, this week's activity is all about thinking about the food that microbes in your Winogradsky column are eating! We look forward to hearing what you find in yours!

5th activity - Environmental Microbiology 101 - The secret lives of microbes on Earth

posted Oct 23, 2017, 4:52 PM by Beth Orcutt

Greetings, microbe adopters. While you are sending in the results from last week's activities about sampling the seafloor (we'll post your results soon), it is time to start something new. Let's learn some more about all of the awesome microbes out in the world! Back in Week 2, you learned about the different shapes and sizes of microbes. In the first week, you also went out "into the wild" to collect some mud for growing microbes in your Winogradsky columns. Now it's time to learn more about what microbes do (including what they are doing in the Winogradsky columns!) and why they are so important.

A reminder of what some of your Winogradsky columns looked like a few weeks ago.

First of all, it might be useful to know that there is an "official" name for the study of what microbes do in the environment, figuring out the identity of microbes and investigating how some microbes interact with each other and life. That name is environmental microbiology. And what would you call a scientist that studied environmental microbiology? If you guessed environmental microbiologist, you would be correct. Totally awesome would also be correct!


So, how do we even know that microbes live in the environment? Maybe you only think of microbes as gross, germ-y things that can make you sick, and that you have to take antibiotics to get rid of. Or maybe you think of them as the weird things that live in your yogurt (you know, those "live and active cultures" that the yogurt containers talk about?). Well, guess what - microbes are just about everywhere! Bottom of the ocean? Microbes are there! Up in the clouds? Microbes are there! On your skin, in your mouth, and in your stomach? Microbes are there, too!


Scientists know that there are microbes in all of those places by collecting samples and then analyzing them with different instruments. For example, an environmental microbiologist might collect some seawater and then filter or strain it through a thin piece of mesh paper to collect and concentrate all of the microbes onto the mesh paper. The holes in the mesh paper are only 0.2 micrometers in diameter, so, smaller than the average size of a microbial cell (remember, that's 1 micrometer from Week 2) to keep the cells from going through the holes. Then the scientist could look at that piece of mesh paper under a microscope with a bunch of magnifying glasses to see the microbes up close. Another way an environmental microbiologist might tell that there are microbes in a sample would be to try to grow the microbes in a culture with different food sources — kind of like what you are doing with the Winogradsky columns!


Why is it important to put different food sources into a Winogradsky Column? Well, first of all, let's think about what egg yolks and newspaper are made of. Egg yolks contain different fats and proteins, many of which are rich in the element sulfur. Have you ever smelled a rotten egg? If you have, then you know that a rotten egg smells pretty bad — that bad smell comes from the compound hydrogen sulfide, which forms from the breakdown of the sulfur contained in the fats and proteins in the egg yolk. Some microbes can use this sulfur as an energy source to grow (like we use oxygen as a fuel to burn all of the energy-rich sugars, fats and proteins that we eat). That brings us around to the newspaper. Remember what paper is made of? Hint, hint — trees. Well, what are trees made of? A tree is a plant that uses photosynthesis to fix carbon dioxide from the air and turn it into organic material, like sugars and fats and proteins. Paper is basically a carbon source, then, when fed to microbes.


Just like us, all life on Earth needs to eat different kinds of carbon to get energy, including microbes. And we all need a "fuel" like oxygen to burn the carbon for growth and sustenance. The cool thing is, some microbes have the ability to "breathe" all sorts of interesting chemicals besides just oxygen. Some microbes respire sulfur, others can respire iron, some get energy from hydrogen, and some can even grow using methane (also known as natural gas).


Just like plants, some microbes also have the ability to make organic matter out of carbon dioxide; these microbes are called autotrophs by scientists. Some carbon dioxide-fixing microbes also use sunlight to get energy for this process, just like plants — they are called photo-autotrophs. Others can use chemical energy to make carbon dioxide fixation happen — they are called chemo-autotrophs. Not all microbes make their own organic matter, though — just like we don't. Instead, those microbes eat the organic matter that other microbes have made - they are called heterotrophs. Photoautotrophic microbes are very important for us — through photosynthesis, which produces oxygen from water, they produce roughly half of the oxygen in the air that we breathe. Another way to think of that — for every other breath that you take, microbes made that oxygen!

Example of layers that develop in a Winogradsky column.


How else are microbes important to us? Well, every time that you flush a toilet, the waste goes to a waste water treatment plant if your house is connected to the city sewers. Special microbes live in those waste water treatment plants, and they help to break down your waste to make it less toxic to the environment. Another example is found in your gut! Microbes living in your stomach help to break down the food that you eat. In fact, did you know that at any given time there are more microbe cells in your body than human cells, maybe almost ten times more? Microbes help to keep you healthy, although some can make you sick if they get out of control.


Step 1: Have a look at your Winogradsky column, and maybe look at the photo of it that you took when you set it up. Have you noticed color changes? Have you noticed any unusual odors? Any other observations?


Step 2: Compare your Winogradsky column layers with those in the figure. Do you see any of them? What kind of microbes do you think live in these layers? Where do you think aerobic and anaerobic microbes live in the Winogradsky column?


Step 3: Take a photograph of your Winogradsky column and email it to deepmicrobe (at) by Sunday, October 29, along with your observations of what layers have developed, and your answers to the math questions below.


And now, for some math fun! Try to figure out the answers to these questions and send us your answers.


We are currently on an oceanographic expedition to try to figure out which microbes are living in the hard, rocky crust of the seafloor, and to understand what they are eating to survive and thrive. Although the oceanic crust is a huge undersea aquifer where microbes live, we know very little about them at this point. Some clever scientists calculated that roughly 10 to the power of 29 (10^29, or 1 with 29 zeroes behind it) microbes are ‘buried alive’ in the deep oceanic sediments that blanket the rocky crust at the seafloor. That’s a lot! 


If we consider that each microbe is, on average, 1 micrometer in diameter, and that there are 10^29 microbes in deep sediments, how long would a string of sediment microbes be if you placed them end to end?  For reference, 1 micrometer is 10^-6 meters, or 0.000001 meters. 

Length: ___________


Would this invisible string of microbes reach from the Earth to the Sun?  For reference, the distance from the Earth to the Sun = 1 astronomical unit = ~1.5 x 10^8 kilometers or 1.5 x 10^11 meters.

Yes or No?__________


On average, one teaspoon full of deep, dark ocean water contains fifty thousand (50,000) microbes. Crazy, huh?! Ok, so the global volume of deep, dark ocean has roughly 200 sextillion teaspoons of seawater – that’s 200,000,000,000,000,000,000,000 teaspoons, or 2 x 1023.  So, roughly how many microbes are there in all of the deep, dark ocean?


Total number of microbes in the dark ocean: __________


There are 52 people sailing on the RV Atlantis for this cruise. Each cruise usually lasts 30 days.  Assuming that each person uses about 50 sheets of toilet paper a day, and that an average roll of toilet paper has 500 sheets, how many rolls of toilet paper does the ship have to carry to meet everyone’s needs for this cruise? ________

4th activity - Sampling the Seafloor

posted Oct 17, 2017, 6:44 AM by Beth Orcutt

Greetings, microbe adopters! Thanks for sending in your projects about defining the ocean seafloor features and high-pressure conditions. In this week’s activities, you will explore the concept of buoyancy and how this is important for conducting research at the bottom of the ocean, and then you will learn a bit about the materials that make up the seafloor, and how microbes live within them.


Buoyancy and density


Have you ever wondered why some things float in water, and others sink? The answer has to do with density (an object’s mass compared to its volume). An object’s density, compared to the density of the surrounding environment, determines whether it sinks or floats. Water has a much higher density than air and can therefore apply more pressure on objects. This is true not only when an object descends in the water but also when an object is supported in the water by floating. The pressure of all of the water below an object pushes up on the object. That pressure is greater than the downward pressure exerted by gravity. A boat, while its materials may be denser than the water, uses its shape to distribute that pressure in such a way that the upward pressure exceeds the downward pressure.  Not until the object overcomes the pressure of the water does the object sink (like when the Titanic filled with water). Buoyancy force is the upward force exerted on an object. Objects that float on or toward the surface of the water are said to be positively buoyant.  Objects that sink are negatively buoyant.  Objects that hover, that is, neither rise nor fall, are said to be neutrally buoyant.  

 Scientists using submarines and ROVs like Jason need to be able to have those objects sink to the seafloor, be neutrally buoyant to do work, then become positively buoyant so they can return to the surface. How do ROVs do this? The submarines and ROVs initially have extra disposable weights on them at the beginning of a dive. The weights help the ROVs sink to the seafloor. Once at the bottom, they drop some of the weights to achieve neutral buoyancy. At the end of the dive, the rest of the weights are dropped to make the ROV positively buoyant so that it will float back to the surface.


Sediment and Rocks


ROVs and submarines are invaluable tools for scientific research at the bottom of the ocean, especially for scientists interested in studying microbes that live down there. For example, the "arms" on the ROVs and submarines (called manipulators) are used to collect samples of sediment, rocks, and fluids at the bottom of the ocean, from the different habitat types introduced in Week 3. This is one of the only ways that scientists can collect samples with microbes from these environments.

Example of life on the seafloor amongst sediment and rocks, from the Dorado Outcrop in the Pacific Ocean.


In deep marine sediments, there are between one thousand to one billion microbial cells in every cubic centimeter (about a quarter of teaspoon) of sediment. These microbes are dependent on the delivery of chemicals through the sediments to find energy to grow, and these chemicals travel differently depending on the sediment types. The rate at which water moves through sediments and rocks (discussed here on the Giant Microbe update) to bring nutrients and food has profound effects on the abundance and growth of microbes in the deep ocean. In the activity, you will test how particle type and size affects the rate at which water moves through materials.


Deep microbes also live on rocks beneath the seafloor. Like sediment microbes, they are dependent on chemicals to gain energy. Some microbes can mine chemicals directly out of the rock, while others use chemicals in the water moving through the cracks in the rocks. Rocks have different reactivity, which means that they release dissolved ions and gases out of the solid rock matrix at different rates. For example, both the basalt and pyrite rocks contain iron. Basalt is an igneous rock and one of the most abundant rocks types on earth. Pyrite (fool’s gold) also contains a lot of reduced sulfur. Microbes could use the iron and sulfide out of these rocks to grow. Calcite is formed under conditions where carbonate ion (formed from the dissolution of carbon dioxide) is pulled from the environment to form the shells of living organisms, for example, corals. To explore the differences in rock reactivity, you will do an experiment to examine the reactivity of your three rock samples - basalt, pyrite, and calcite - in relation to changes in pH, or the concentration of hydrogen ions in fluids. 

[Note: a more detailed version of this week's activities, for use by an instructor in a classroom, can be found at the week 4 link here

Activity 1: Buoyancy of water


Materials needed:

- Large (18 gallon) Rubbermaid-type tub to hold water, or small "kiddie" pool, or a trashcan.

- Three 1 liter water bottles with caps (an empty soda bottle would be perfect)

- Funnels

- Beaker or similar for measuring 50 milliliter volumes. Can substitute ¼ cup measuring cup.

- Three small plastic containers to hold ~0.5 cup (like Glad® mini round)

- A large mixing bowl or bucket that is wide and deep enough to dip the small plastic containers in

- Food coloring

- Spoon

- Table salt

- Rubbing (isopropyl) alcohol: Handle with care! See safety precautions at

- Water

- Rubber kitchen gloves (optional)

- Balance (optional)


Step 1: Fill the large plastic tub or trashcan with water.  


Step 2: Figure out how much water you need to add to the empty bottle to get it to hover in the water in the trashcan – not floating on the surface or sinking to the bottom. To do this, add 50ml (or ¼ cup) of water to the bottle, cap the bottle, and then test it in the tub. If it still floats, add another 50ml and try again, and repeat this until you find the amount to achieve hovering. Questions: How much water did you have to add to your bottle? Was the bottle negatively, neutrally, or positively buoyant when it was floating?


Step 3: Pour water into the large bowl or bucket, and add a few drops of one color of food coloring.


Step 4: Fill up one of the small plastic containers completely with the colored water by dunking both the container and lid under water and closing while underwater. Important: Try to keep out any air bubbles. Wear gloves if you want to avoid the food coloring.


Step 5: Dump out the remaining water in the bowl or beaker, add some more water to the bowl or bucket, add a few drops of another color of food coloring, then add 2 heaping tablespoons or ¼ cup of salt (to make saltwater). Fill up another small plastic container in the same manner as described above. Wear gloves if you want to avoid the food coloring.


Step 6: Dump out the remaining water in the bowl or beaker, fill the bowl or bucket with rubbing alcohol, add a few drops of another color of food coloring, and then fill up another plastic container. Wear gloves if you want to avoid the food coloring. Now you should have three containers - one with freshwater, one with salt water, and one with rubbing alcohol.


Step 7: Place each container with food coloring into the tub or trashcan with water. Questions: Which ones floated, hovered, or sank? Which one was positively, negatively, or neutrally buoyant? Which one had the lowest density? Would an ROV that can sink in freshwater be able to sink in saltwater?


Activity 2: Sediment and Rocks


Materials needed:

- Small glass bowl or cup

- Spoon

- Vinegar

- Water

- Magnifying glass or hand lenses

- piece of white paper

- The following items come in the kit from GSME coordinator Kirstin. If you do not have access to these materials, you can also purchase soil, sand, and gravel from a local hardware store.

- Glass vials with screw caps (Available from Wards Geology: $14.20 for 12 pack, 8 ml size, part 6356502)

- Basalt rock student specimens: (Available from Wards Geology: $11.50 for 10 pack, part 471037 )

- Pyrite rock student specimens: Available from Wards Geology: $16.95 for 30 pack, part 466446

- Calcite rock hand samples: (Available from Wards Geology: $9.95 for testing chips, 30 pack, part 461421)

- Soil, sand, and gravel set: (Available from Wards Geology: $39.95 for 32 oz jars of each sediment type, part 451990 )

Piece of white paper


Step 1: Pick up samples of basalt, pyrite, and calcite. Look over the samples with hand lens and make observations about their composition.


Step 2: Pour roughly 1-cm-deep (roughly half an inch) layer of water in the dish. Place a piece of basalt in the water. Describe how the water travels, clings, soaks, etc. to the basalt. Repeat with the pyrite and the calcite rock samples. Questions: Which rock substance seems to absorb/retain the most water, and which the least?


Step 3. Dump out the water and pour a 0.5-cm-deep (roughly ¼ inch) layer of vinegar in the dish. Be careful - vinegar has a strong odor - don't breathe in too deeply! Gently place each rock type into the vinegar and watch for any evidence that the rock is reacting with the vinegar. Questions: Which rock reacts with vinegar? Why do you think that might be, considering that vinegar is a weak acidic solution?


Step 4: Pour a little bit of sand and soil samples out on a piece of white paper and observe the particles with your eyes and the hand lens. Questions: What differences do you see? Which particle type do you think is more likely to allow water to move through faster?


Step 5: Pour about a 2-cm-thick (~1 inch) layer of soil into the bottom of the glass vial. Tap the vial gently on the palm of your hand to settle the soil particles. Next, pour another 2-cm-thick layer of sand on top of the soil, and again tap gently on your hand to settle. Next, gently add water to the top of the sand until you fill up the rest of the space in the vial. Questions: What difference do you notice between how the water interacted with the soil and the sand? Did this match your prediction?


Step 6: Judging from your results of the water moving through the sand and soil, choose an “ideal substance” for growth and nutrition for microbes and defend your answer. Judging from your results of the reaction of rocks with acidic solutions, choose an “ideal substance” for growth and nutrition for microbial communities in the oceanic crust and defend your answer.


Step 7: Draw a picture of what you think microbes living on rocks or in sediments would look like.


Step 8: Take a picture of your drawing, and email that along with your answers to Step 6 to deepmicrobe (at) by Sunday, October 22, 2017.

Your ocean features!

posted Oct 16, 2017, 5:09 PM by Beth Orcutt

Greetings, microbe adopters! We hope that you had fun learning about the features and pressure of water at the bottom of the ocean. As part of the activity, you thought about how many gallons of water would be stacked on your chest to equal the pressure that you would feel if you went to the bottom of the ocean. How many gallons would be in that stack? Well, if the average depth of the ocean is 12,000 ft, and if pressure increases by 14.69 pounds per square inch (the unit psi - sorry, I left out the “per square inch” part!) with every 30 feet, then the pressure at the bottom of the ocean is 12,000ft x 14.69 psi/30ft = 4,996 psi. You determined in your test that a gallon of water, which weighs roughly 8.5 pounds and has a surface area of roughly 50 inches, has a pressure of roughly 0.17 psi. So, at the bottom of the ocean at 12,000 ft, you would feel like you had 4,996 psi x 1 gallon/0.17 psi = 29,388 gallons of water on your chest! Ouch!!


This past week you also learned about the different environments at the bottom of the ocean, and thought about which ones your adopted microbes might live in. I’m really impressed with your diagrams! Violet in Lamoine indicated that her microbes – Arcobacter sulfidicus – would be found in hydrothermal vents: correct!


And Hope in Orland indicated that her microbe – Marinobacter – could be found in deep ocean water as well as within ocean crust: also correct!


We also received an update from Audrey in Cumberland about her great looking Winogradsky column. Grow, microbes, grow!

Awesome. Check back in tomorrow to see the next set of activities!


Another Winogradsky column!

posted Oct 12, 2017, 11:18 AM by Beth Orcutt

Greetings, microbe adopters! A quick update from Hannah in Lewiston about her Winogradsky column. Hannah and her brother both set up Winogradsky columns in week 1 - it'll be interesting to see how they compare to each other.

3rd activity - Features of the seafloor

posted Oct 10, 2017, 5:08 AM by Beth Orcutt

Greetings, microbe adopters! For this week’s activity, you will be learning more about the bottom of the ocean. Read through the information below, and then try out the activities at the end.


World map.


Ocean Basics


Our planet is a water planet - 71% of Earth's surface is covered with water. When you look at a picture of Earth taken from space and notice how much blue there is, you realize that Earth is not only a water planet — it is an ocean planet. The depth of water in the oceans ranges from just a few feet at the beaches down to almost 11,000 meters (roughly 36,000 feet or almost 7 miles!) at the deepest spot in the ocean — the Mariana's Trench in the western Pacific Ocean. The average depth of the ocean is roughly 4,000 meters (~12,000 feet). When scientists multiply the depth of the ocean by the amount of area that the ocean covers on Earth, they determine that the volume of the ocean is approximately 1 billion billion cubic meters, or the size of 40,000 billion Olympic swimming pools. That volume is 170 times the size of all other living space on Earth combined, including land, air, and fresh water environments.


If you have ever been to the beach or out on the ocean, you know that the water tastes salty. That is because ocean water contains many dissolved salts. On average, seawater contains approximately 35 grams of dissolved salt per liter of water, and 90% of that salt is sodium chloride — the same kind of salt you use on your food.



Bumpy Bottom


Not just a big bathtub with smooth surfaces, the bottom of the ocean has many different features, including rocky crust and muddy sediment — the little particles of sand and mud that settle to the bottom of the ocean. In fact, the longest and biggest mountains on Earth are at the bottom of the ocean! For example, Mauna Kea, a volcano off of the Big Island of Hawaii, has its base at the bottom of the Pacific Ocean, with a total height of 9,449 meters (5.87 miles). The longest mountain range in the world is the Mid-Ocean Ridge system that circles the globe. This vast, interconnected mountain chain forms as a result of heat rising from the center of the Earth, pushing apart the oceanic "plates" at the bottom of the ocean. In other parts of the ocean, deep trenches form as one of the plates slides underneath another. This smashing action also builds up heat, forming chains of seamounts and volcanoes, such as the volcanoes that ring the western shores of the USA in northern California, Oregon, and Washington. Seamounts are basically underwater mountains that don't quite reach the surface of the ocean. Closer to the coasts, sand and dirt carried out to sea by rivers settles out as sediment on the seafloor. Heavier particles like sand settle out quickly, forming the sandy beaches you visit on vacation, while lighter and smaller particles like clay get carried farther out to sea, forming muddier sediments at the bottom of the ocean. These deposits of sediment along the coasts form features called the continental shelf — a relatively flat and shallow expanse near the coasts — and the continental slope — a steeper feature that connects the continental shelf with the deeper abyssal plains that cover most of the seafloor.


Cross section of the ocean bottom.



Schematic of a Mid-Ocean Ridge.


Dirty Water Keeps the Light Out


Particles in seawater do more than build sediment at the bottom of the ocean: particles in the water affects the amount of light that can penetrate through — more particles mean less light. Think about opening your eyes underwater in a pool versus in a lake or in the ocean - you could probably see farther in the pool because there are very few particles in the pool. Close to the coasts, where there are a lot of particles in the ocean, sunlight only reaches a few meters into the water, but farther away from land, sunlight can reach almost 1,000 feet deep into the water. As on land, tiny plants living in the water can use this sunlight for photosynthesis — using the energy from sunlight to turn carbon dioxide into organic matter like sugars, fats, and proteins, and releasing oxygen as a waste product. In fact, added together, the tiny plants in the ocean produce almost half the oxygen in Earth's atmosphere, which we humans need to breathe! When these tiny plants, and the tiny animals that eat them, die, they slowly sink down to the bottom of the ocean, mixing with the sandy and muddy particles that came from the rivers.


Life in the Extreme


Remember how the oceans are on average almost 12,000 feet deep, but that sunlight only reaches up to 1,000 feet deep in particle-free water? That means that most of the ocean is dark. Remember how the ocean is almost 170 times larger in volume than all of the rest of the living space on Earth? Together, that means that most of the space for life on Earth is in total darkness! Thus, although it may seem like an alien environment to us, the deep dark oceans are the most "normal" part about life on Earth. So, what are some of the features of this deep dark space? Well, it's dark, obviously, which means no photosynthesis happens there. The absence of heat from the sun also means that it is cold — the average temperature of the deep ocean is just slightly above the freezing point of water, about the temperature of the inside of a refrigerator.


However, there are some places at the bottom of the ocean where really hot water comes spewing out of the seafloor. These places are called hydrothermal vents, and they are often found in association with the Mid-Ocean Ridge. The vents of hot water are the result of water circulation below the seafloor. As on land, where water underground (which we tap into with wells to get water), water also moves through cracks in the rocks below the seafloor, with the movement driven by changes in pressure and temperature in the rocks. As the water moves around beneath the seafloor, it gets heated up from the heat in the rocks and the heat coming from the center of the Earth. The water coming out of hydrothermal vents has been recorded as high as 400 degrees Celsius (~750 degrees Fahrenheit). By comparison, water on your kitchen stove starts to boil around 100 degrees Celsius (~215 degrees Fahrenheit). Often, the hot water at the bottom of the ocean comes out looking like smoke. Scientists classify hydrothermal vents as "black smokers" and "white smokers" because of the color of the so-called smoke, which isn’t a gassy smoke at all but rather the appearance of different dissolved minerals in the hot fluids as they come in contact with the cold seawater. The difference in color is due to different minerals in the fluids, which is a result of temperature - black smokers are hotter than white smokers, and they contain more dissolved metals like iron and copper.


Example “white smoker” hydrothermal vent.


Example “black smoker” hydrothermal vent.



The Pressure of Life in the Deep


So, how does the water at the bottom of the ocean remain fluid (and not steam) at such high temperatures?! Pressure is the answer! Here at the surface of the Earth, we experience a pressure we call 1 atmosphere, or atm. Pressure increases by 1 atm with every 10 m (30 feet) of water depth. Hydrothermal vents occur at the bottom of the ocean, at depths as deep as 5,000 meters, which would have a pressure of ~500 atm, or over 7,000 pounds per square inch. As pressure increases, the boiling point of water also increases, allowing hydrothermal fluids to still be liquid at such high temperatures. Humans using SCUBA equipment can only dive about 100 feet without needing to wear special protection against pressure. To get to the bottom of the ocean to study hydrothermal vents and deep, dark life, scientists have to use much more specialized equipment like submarines and robots, which you will learn more about in another lesson.


Remember the microbes you learned about in the last lesson? Well, microbes live in all of these different environments at the bottom of the ocean, including in the deep dark seawater, in the hot hydrothermal vents, in the muddy sediments, and even in the hard rocks below the seafloor! You will learn more about those microbes in the next lesson.


Ok, here is this week’s activity about pressure at the bottom of the ocean. (NOTE: For an instructor version of this exercise to use in a classroom or with a group, with more detailed questions and answer sections, please see the online tutorial posted on the Overview of Activities section of the website here)


Step 1: Download a copy of the Ocean Features handout and the UnderPressure handout.

Step 2: Cut out and color the different ocean feature pieces, and then assemble them.

Step 3: Indicate on the assembly where you think that your adopted microbe lives, and then take a photograph of the picture.

Step 4: Fill out Part 1 on the Under Pressure handout.

Step 5: Fill up 1 gallon milk jug with water. Estimate how much it weighs, then weigh it on a scale to check your guess.

Step 6: Lie on the floor on your stomach and have someone place the full one gallon jug of water on your back. How does this weight affect your breathing? How much pressure did this gallon put on your back, in pounds per square inch?

Step 7: Try to figure out how many gallons of water would be stacked on your chest to equal the average pressure at the bottom of the ocean? Remember from above that the average depth of the ocean is ~4,000 meters (~12,000 feet), and the reading material tells you how to calculate the increase in pressure with depth.

Step 8: By Sunday, October 15, email deepmicrobe (at) with a copy of your picture of where you think your microbe lives, and your answers to the questions about the pressure of water.

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