Microbiology > Pondlife: Our Tiny Neighbors

Pondlife Episode 1

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[ELECTRONIC MUSIC AND SOUND OF WATER DROPLET]

[MICROSCOPE SLIDE CLICKS INTO PLACE]

[BOUNCY, ELECTRONIC MUSIC]

SALLY WARRING (microbiologist): My name is Sally. I am a biologist at the American Museum of Natural History where I study microscopic organisms.

On Pondlife we are going to go on a safari to explore the microbial wildernesses that exist all around us.

I’m in the middle of Manhattan. I’m at the Harlem Meer in Central Park and I’m here to look for a particular microbial community. It’s a community that you might have seen before, but you’ve probably not looked at it quite like this.

For most of human history, people thought of all life as being plants and animals. And the fact that species existed that were so small that you couldn’t even see them was completely unknown.

That all changed in the Seventeenth Century when a Dutch fabric designer named Antonie van Leeuwenhoek invented the most powerful microscope the world had ever seen.

I have a replica of his microscope in my pocket. This is it. This tiny little thing contains a really small spherical glass lens and that spherical glass lens was capable of magnifying up to 300 times.

So, he would place he was interested in on one side of the lens. He would look through by placing the microscope right up to his eye.

So, using this microscope he became the first person to see unicellular life, and he first saw that unicellular life when he looked at a community of microorganisms called pond scum. And I can see a beautiful example right over here.

[BUBBLY ELECTRONIC MUSIC]

WARRING: This is great…

This is exactly what we’re looking for.

Beautiful pond scum.

Success!

That pond scum is a growth of filamentous green algae and I’ve put some here on my Leeuwenhoeck microscope and we’re going to take a look and see what he might have seen in the pond for the first time.

Leeuwenhoeck learned by looking through his microscope that the pond scum was made up of green algae that wound together. But what amazed him the most was that moving amongst that green algae were tiny little creatures. He called those little creatures animalcules or “little animals.”

These days microscopy and our understanding of microbiology have come along way. I have with me a modern-day field microscope. Rather than a small spherical lens it has an objective. An objective contains many glass lenses stacked one on top of the other.

We’re gonna take a look at what we’ve got.

At one hundred times magnification we can really see the details of the green algae.

It’s called spirogyra.

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WARRING: Each spirogyra filament is one cell thick, about the width of a human hair.

Spirogyra gets its name because inside each cell there is a long, thin, green chloroplast that coils and gives the organism its corkscrew appearance.

Spirogyra, like all algae, live off sunlight.

But when they grow in dense mats like the one in the Harlem Meer the filaments on top end up shading the ones beneath. 

But Spirogyra has a way of dealing with this.

The filaments are able to glide and stay constantly on the move.

This way each filament will, at least for part of the time, have access to the sun.

Just like Leeuwenhoek we find many microbial creatures living among the algae.

Here there are several species of ciliate.

Ciliates are a diverse group of single cellular organisms that are covered in small, hair-like structures called cilia

Each species of ciliate has a unique arrangement of cilia.

This one has cilia only on the underside of its cell.

It uses the cilia like tiny legs to walk about on the spirogyra.

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WARRING: This is one of the ciliates that Leeuwenhoek was first to describe.

It’s called Vorticella

Each is an individual bell-shaped cell sitting atop a long stalk.

That stalk is rather special.

It’s a curious coiling contraption that can move like lightning if the cell senses any danger.

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WARRING: The stalk also keeps the Vorticella anchored, so that it can use its cilia to generate a current in the water.

The cilia are arranged in a ring around an opening in the cell that acts as a mouth.

The cilia beat and drag water, bacteria, and other small microbes right into the Vorticella’s waiting mouth.

This beautiful organism is a heliozoan—“helio-“ meaning sun and “-zoan” meaning animal. Though, it’s not an animal at all.

The heliozoan is covered in many spike-like structures called axopodia, which radiate out from the cell’s surface and act as a net for ensnaring prey.

In real time the heliozoan appears static, but in time lapse it really comes to life.

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WARRING: A green cell is ensnared…

but makes a lucky escape.

The second cell is not so lucky.

Leeuwenhoek was fascinated by organisms that moved like animals, but were green like plants.

This one is called phacus.

It’s not an animal, or a plant. It belongs to a completely separate group of organisms called the euglena.

Its movement is due to long, thin structure called a flagellum that extends out the front of the cell.

The flagellum beats and pulls the cell through the water.

You can also catch a glimpse of a red spot inside the phacus. 

This is called an eyespot. 

It sits at the base of the flagellum and can detect the intensity and direction of light.

Like a plant the phacus lives off sunlight and this eyespot allows it to move through the water to wherever the light intensity is best. 

[LILTING ELECTRONIC WALTZ]

WARRING: In that one drop of water we just saw a wide variety of microbial species. In the whole pond their numbers probably reach into the many thousands. And that’s only scratching the surface of the amount of microbial diversity that we could find the world over. And to really get a handle on this microbial diversity, we’re just going to have to keep exploring.

I’m gonna put these microbes back where I got ‘em from.

[Credits roll.]

Pondlife Episode 2

[ELECTRONIC MUSIC]

[SOUND OF WATER DROPLET]

[MICROSCOPE SLIDE CLICKS INTO PLACE] 

SALLY WARRING (microbiologist): We are surrounded by hidden microscopic worlds filled with fascinating life forms.

Thousands of microbial organisms live within a single drop of water.

On Pondlife, we’re going on a safari to explore the microbial wildernesses that exist all around us.

Today I’m out looking for a group of organisms that evolved over two billion years ago.

These organisms were the first to live by photosynthesis. That’s the process of using sunlight to make sugars and then those sugars are used to power the cell.

A byproduct of photosynthesis is oxygen, and two billion years ago these organisms became so abundant that they completely changed the Earth’s atmosphere.

It went from one that was very oxygen poor, to the oxygen-rich atmosphere that we live in today.

These microbes are called cyanobacteria and lucky for me, they are just as abundant today as they were two billion years ago. 

In fact, I haven’t had to go very far at all to find them.

I’ve simply walked out the door, I’ve crossed the road, and I can already see a pond that is teeming with cyanobacteria.

[BUBBLING ELECTRONIC MUSIC]

WARRING: You can find cyanobacteria all over the world.

There are currently around 3,000 described species with different morphologies and habitats from freshwater ponds to arctic oceans.

They even live in soil.

As I wander around Central Park, I’m on the lookout for signs of cyanobacteria.

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WARRING: It’s cyanobacteria that are making this pond so green.

If you look closely at this water sample, you can see that it’s full of tiny, floating, green particles.

Each one of those particles is a colony of cyanobacteria and each one of those colonies is made up of multiple individual cyanobacterial cells living together.

To find out what species of cyanobacteria is living here I’m going to have to put it under the microscope.

The cyanobacterium blooming in the Lake belongs to the genus Microcystis.

Microcystis colonies are made up of many individual cells suspended in a clear mucus.

A colony may start as one cell… which divides to become two cells… then four… and so on until some colonies are large enough to see with the naked eye.

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WARRING: The colonies grow fast in warm summer waters, and when their numbers get dense enough, we call this a bloom.

Many cyanobacterial species are bloom-forming, and you can distinguish each species by their unique colony shapes.

One advantage of living as a colony is that when many individuals live together, tasks can be divided among the members.

We can see this in another cyanobacterium from the lake.

This one belongs to the genus Dolichospermum, and among its helical colony, some cells look a little different from the rest.

These specialized cells are called heterocysts and they have given up their photosynthetic ability to focus on the task of absorbing nitrogen.

They build that nitrogen into molecules that can be shared and used by all the cells in the colony, and in return the other cells share the sugars gain through photosynthesis with the heterocyst.

By dividing up these tasks, each is run more efficiently, and the colony can prosper.

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WARRING: Thousands of visitors walk through Central Park every day, mostly unaware of the many tiny dramas playing out all around them.

With a microscope, we can catch a glimpse into these unseen worlds.

The bloom in the next pond is dominated by a cyanobacterium from the genus Aphanizomenon.

Aphanizomenon forms long, thin, filamentous colonies.

And while at first they appear to only drift, under time lapse we can see just how busy they are.

[RUSTLING ELECTRONIC SOUNDS]

WARRING: There is a good reason to stay on the move.

Cyanobacteria sit at the base of the food chain and are good eating for a number of small predators. 

This ciliate is a specialist cyanobacteria predator.

It’s from the genus Nassula and it’s using its sensitive cilia to feel out a filament, searching for an end.

Once located, it begins its work, sucking in the cyanobacteria like a strand of spaghetti.

[WHIRRING ELECTRONIC SOUND]

WARRING: As the cyanobacteria get ingested the filament bends and breaks, allowing it to fit inside the rotund little ciliate.

[WHIRRING, SLURPING ELECTRONIC SOUNDS]

WARRING: This process can take a little time, especially if the filament is particularly long.

The ciliate keeps going… and going…and going…and going…and going, until the cyanobacteria are completely swallowed up.

Delicious.

[BUBBLY ELECTRONIC MUSIC]

WARRING: When I’m out looking at these microbial communities, I often see things that I want to take a closer look at and there’s only so much I can do out in the field with my portable microscope. So, when I see something interesting, I take a sample and that comes with me back to the museum and into the lab.

[BUBBLY ELECTRONIC MUSIC]

WARRING: While I’m working with the pond water, I want to keep everything sterile.

This is because I don’t want microbes that might be growing in the lab or on me to end up growing in my lab cultures.

Now that the microbes are out of the pond and in the lab, I also need to make sure they have everything they need to survive.

The bottles here contain different types of growth media. Each medium contains vitamins, minerals, and salts that microbes need.

This big thing is a biosafety cabinet and it’s going to help me keep everything sterile.

I wiped everything down with ethanol before it went into the cabinet, but it also has this wall of air that passes from this vent at the bottom right up the front and that prevents any microbial spores that might be in the air from travelling though into this cabinet.

At the same time, the cabinet is constantly sucking air up through a vent in the top and that means that if any microbial spores do make it through into the cabinet, they get sucked up into that vent rather than landing on my cultures.

I add a small amount of pond water to liquid medium or spread some out onto an agar plate.

That agar plate contains growth medium too, but it’s been solidified by the addition of agar—a kind of jelly-like substance that’s produced by certain seaweeds.

Some microbes prefer to grow on the solid surface of the agar, while others grow better suspended in the liquid medium.

I keep those cultures in a growth chamber, the growth chamber maintains the temperature and provides a constant amount of light each day.

Cyanobacterial blooms can cause real problems, some produce toxins that are lethal to many animals.

I’m interested in the microbes that thrive here, organisms like these flagellates, and this euglena algae, or this collodictyon, all living among the bloom.

Over the next few weeks some of these microbes will grow in numbers, until eventually I can isolate and identify individual species from those liquid cultures, and from the agar plate. 

I’m hoping that by growing and studying some of these microbes that are present in the cyanobacterial blooms that we’ll learn more about the blooms as communities and that we can understand some of the things that are causing these extremely common phenomena.

Even our biggest cities contain microbial ecosystems that are vibrant and complex.

Growing these organisms in the lab helps me to understand just what thrives in this microscopic metropolis.

Pondlife Episode 3

[ELECTRONIC MUSIC]

[SOUND OF WATER DROPLET]

[MICROSCOPE SLIDE CLICKS INTO PLACE]

[BOUNCY, ELECTRONIC MUSIC]

SALLY WARRING (microbiologist): We are surrounded by hidden microscopic worlds filled with fascinating life forms. A handful of soil contains countless microbial creatures.

On Pondlife, we’re going on a safari to explore the microbial wildernesses that exist all around us.

On this episode of Pondlife we are on a field trip. We’re about an hour and a half north of the city at the Mohonk Preserve. 

I am here with Michael Tessler from the American Museum of Natural History and we are here to look for two things that we both really like, mosses and microbes. 

MICHAEL TESSLER (molecular biologist): Yeah, thanks so much for having me, Sally. I’m really excited to poke around on some rocks and some trees and look for lots of fun little mosses.

Mosses are wonderful tiny plants and they are also some of the earliest life forms to have colonized land. 

WARRING: Moss are often the first to colonize a bare surface like a rock or a tree trunk, areas where water and nutrients can be in short supply.

Moss have adaptations that allow them to thrive in these environments. But they don’t do it alone, they have microbes to help them out.

TESSLER: Right yeah so let’s check out some rock mosses.

WARRING: Oh, wow.

TESSLER: So, this one’s a cool moss. This is Hedwigia. And if you take a little piece and look at it under your hand lens, you’ll see that a lot of it is see-through.

Mosses are some of the most interesting looking things under the microscope.

WARRING: Well, of course I didn’t come on this trip without bringing a microscope…

TESSLER: Yeah

WARRING: …so do you want to take a look?

TESSLER: Definitely, let’s do it.

There’s so many shapes and sizes and weird things going on with mosses that, you know, you’d never know just looking at them when you walk by.

Get some of these tiny little leaves off.

WARRING: I have this phone adapter.

TESSLER: Oh yeah that’s awesome. You can see the leaf cells. That’s cool.

WARRING: Yeah.

TESSLER: So, this is the leaf and this is the leaf tip and you can see it’s kind of see-through—all the cells. They don’t have chlorophyll in there.

WARRING: Under the microscope we can see just how thin a moss leaf is.

Each consists of only a single layer of cells.

These thin leaves can absorb water and nutrients directly from their surroundings, rather than having to transport water and nutrients from the soil through roots and shoots, like larger plants.

For these rock-dwelling species, this means they can soak up rain water and even morning dew directly from the rock.

Ok, so we’re going up to four hundred times magnification now…

TESSLER: Yeah.

WARRING: …and we’ll take a look.

TESSLER:  Isn’t that cool?

WARRING: That’s awesome so what are those little things?

TESSLER: Yeah, they’re just like little projections of the cell and a lot of mosses have these weird little projections on the cell. Again a lot of things that grow on rock have things like that…

WARRING: Okay.

TESSLER: …in kind of these harsh environments that dry out or potentially get a lot of sun.

WARRING: These microscopic structures on the moss leaves might be playing a role in hydration, creating small channels and depressions to hold water.

These spongy leaves also make an excellent environment for microbes, like these cyanobacteria, nestled here in the curve of a tiny leaf.

So, one of the other things I want to do is try to collect a concentrated sample of microbes from this moss. So, shall we give that a go?

TESSLER: Oh, definitely yeah.

WARRING: So, the microbes will be living on the moss and around the moss and one of the ways we can attempt to concentrate them and kinda tease them out from the moss is to take a little bit of water and just kind of flush that water over the surface of the moss and pull it back up into this pipet and hopefully, we will be able to trap some microbes.

Alright, so I can see lots of bacteria.

As the moss grows, it sheds dead cells, which are broken down by fungi and bacteria, over time forming a soil layer.

This soil layer contains moisture and nutrients from the decomposed tissues, providing more habitat for more microbes.

Cyanobacteria are here, too. These photosynthetic bacteria can play an important role in this community.

Their metabolic activity provides much-needed nitrogen that the moss and microbes can use.

Oh, here we go.. what’s this?

TESSLER: Is that a ciliate?

WARRING: That is a ciliate, yeah…

TESSLER: Oh, very cool

WARRING: A tiny wee one.

Ciliates are single-celled predators that live by eating bacteria and other small microbes in the soil, this way contributing to the nutrient cycle.

The diversity of ciliates we can find in this one patch of moss is astounding. Long ones, round ones, red ones, and even green ones packed full of symbiotic algae.

So, what’s amazing, right, is that these organisms, like ciliates, which need to be submerged in water to survive, are able to make a living on something that dries out periodically like a moss. And one of the reasons they’re able to survive is because they’re so small. So, even when this moss gets quite dry there can sometimes be microdroplets of water around its leaves and a ciliate can survive quite a long time in a microdroplet of water.

Not all the microbes here are single cellular. Some are tiny multicellular animals and—just like us—they come complete with a complex digestive system including a mouth, stomach and intestines.

They even have small brains and simple nervous systems.

This animal is a rotifer.

Rotifers have a single foot at one end that helps with movement and attachment to surfaces.

At the other end is a crown of cilia that funnels water and particles through the mouth and mastax. The mastax is a simple pharynx that moves the incoming particles through to the stomach.

This is a nematode, a microscopic worm living here in the soil. Nematodes are some of the most numerous animals on Earth. Thousands can exist in a single handful of soil.

One of the more charismatic microscopic animals is this one. This is the tardigrade, commonly known as the water bear or moss piglet.

This tiny critter is a common resident of mossy soils where it sucks up food through a tubular mouth.

Each tardigrade possess four pairs of stubby legs, complete with tiny claws.

Though not exactly graceful, these legs and claws do help the tardigrade to move through its microscopic jungle home.

Moss provides a habitat rich in food for these microscopic animals, all of which feed on bacteria or small microbes or moss cells.

In return, their feeding activity contributes to the nutrient cycle in the soil, adding to the breakdown of large organic molecules into smaller ones that can be reused by the moss and the wider community.

However, when the moss dries out, these microscopic animals can dry out, too. But like some of their larger relatives, they possess a thick outer cuticle which serves to protect their soft bodies from fluctuations in temperature and moisture levels.

So, what will happen is that when the moss completely dries out and the rotifers and the nematodes dry out, too, they go into this dormant state where they just live as these inactive things and then the next time it rains they rehydrate and then they become active again.

TESSLER: Which is basically what the mosses do.

You can actually, potentially have a ten-year-old moss, put a droplet of water on it and it will start photosynthesizing immediately after that.  

WARRING: Together, the activity of the moss and the microbes forms a thriving, balanced community, one that can make the most of many environments.

Today we’re not just here to look at the microbes and the moss through the microscope. We’re also going to collect some of these mosses and take them back to the lab with us, where we’re hoping to extract DNA from all the organisms that are living amongst the moss and use that DNA to help us identify what the different organisms are that make up this moss community.

TESSLER: Why thank you, Sally

WARRING: No problem

So, we’ve been out, and we’ve collected all these moss samples because we’re really interested in exploring this question of microbial diversity in association with moss.

Some of this diversity we can see when we look through the microscope. But a lot of the time when we’re looking through the microscope, we don’t actually know what the species are that we’re looking at and we can only look at a really small amount of moss at a time.

So, to try to explore this question of microbial diversity and moss in more detail we’re going to use a technique called metabarcoding.

Here’s moss number one.

TESSLER: Metabarcoding is this great technique where you can look at a uniform fragment of DNA across all the organisms in your sample and you can compare it to DNA sequences from known species and wind up with identification to the species level or at least the family level

WARRING: Our process involves taking the moss and washing it through some sterile water and that detaches all the microbes from the moss. We then take that water and pass it over a really fine filter and the microbes get trapped on that filter.

TESSLER: So that sounds kinda cool, but a little bit complicated. Why not just, you know, look at the moss itself?  

WARRING: The problem is, if you just take a moss and put that through a DNA extraction protocol, you’ll just end up with a ton of moss DNA rather than microbial DNA. So, this water washing, and filtering step helps to elevate the number of microbial sequences in our sample, so we sequence microbes rather than moss.

So, that filter gets taken and then put through a process to extract and concentrate DNA and it’s that DNA that we then send off for sequencing, and then we get our sequences back and we can map them, as you said, and look at exactly what species were present in the moss.

TESSLER: It was impressive to see how many microbial species were living on and around those moss samples and that’s something that’s really under-studied.

WARRING: Yeah, that’s right and I think that some of the work we’re doing in the lab is hopefully gonna increase our understanding of what microbial diversity is really like in a common moss.

TESSLER: Shall we?

WARRING: We still so much to learn about microbes and microbial diversity. Through the microscope, we meet some of the more common species, while laboratory techniques like metabarcording, expand our ability to explore our planet’s extraordinary microbial diversity.