Searching For Microbes In Moss - Pondlife Ep 3

PONDLIFE - Episode 3

[ELECTRONIC MUSIC]

[SOUND OF WATER DROPLET]

[MICROSCOPE SLIDE CLICKS INTO PLACE]

[BOUNCY, ELECTRONIC MUSIC]

[The camera pans over the streets of New York City, in front of the American Museum of Natural History.]

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

[WARRING and a colleague, MICHAEL TESSLER, descend the steps of the American Museum of Natural History.]

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

[The two get into a car at the entrance of the American Museum of Natural History and the engine [REVS] as they start the car.]

WARRING: On this episode of Pondlife we are on a field trip.

[Pan over a hilly green landscape of New York state.]

WARRING: We’re about an hour and a half north of the city at the Mohonk Preserve.

[A lush green forest. Lower third reads: “Mohonk Preserve. New York.” WARRING and TESSLER walk on a path through the forest.]

WARRING: I am here with Michael Tessler from the American Museum of Natural History–

[WARRING and TESSLER appear on screen, speaking to camera, inside the Mohonk Preserve.]

WARRING: – 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.

[Lower third reads: “Michael Tessler”]

TESSLER: I’m really excited to poke around on some rocks and some trees and look for lots of fun little mosses.

[WATER BABBLING]

[Close-up of moss near the water’s edge, followed by a wide shot of moss near a stream.]

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

[MUSIC]

[Camera focuses on moss growing on a tree trunk.]

WARRING: Moss are often the first to colonize a bare surface like a rock or a tree trunk,

[Close-up of tiny moss stalks sticking up out of the green mass.]

WARRING: areas where water and nutrients can be in short supply.

[Close-up of different, leafier-looking moss.]

WARRING: Moss have adaptations that allow them to thrive in these environments.

[A light colored, almost white moss.]

WARRING: But they don’t do it alone, they have microbes to help them out.

[CRUNCHING OF LEAVES AND GRASS]

[A boot steps on some grass and moss. TESSLER and WARRING sit on a moss-covered rock together.]

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

WARRING: Oh, wow.

[Close-up of the moss on the rock.]

TESSLER: So, this one’s a cool moss. This is Hedwigia.

[Text appears: “Hedwigia”. TESSLER pinches off a piece of moss from the rock they’re sitting on.]

TESSLER: And if you take a little piece

[WARRING takes the piece of moss and looks at it through a hand lens pressed to her eye.]

TESSLER: and look at it under your hand lens,

[Close-up of magnified bit of moss held in fingers. The light shines through the moss fronds.]

TESSLER: you’ll see that a lot of it is see-through.

[TESSLER appears back on screen, speaking to WARRING]

TESSLER: 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.

[Camera focuses on tiny moss fronds.]

TESSLER: There’s so many shapes and sizes and weird things going on with mosses that,

[A leaf on top of a mat of moss.]

TESSLER: you know, you’d never know just looking at them when you walk by.

[WARRING and TESSLER put moss leaves onto a portable microscope.]

TESSLER: Get some of these tiny little leaves off.

WARRING: I have this phone adapter.

[WARRING holds the portable microscope with phone adapter, which shows a blown up green moss leaf. WARRING and TESSLER look at the microscope together.]

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.

[Video from the microscope shows transparent leaf cells at the tip. The slide changes to a green section, with green, lumpy-looking cells. A line comes from one cell and text appears: “Moss cell”]

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

[A transparent layer of rows upon rows of cells. Another line appears pointing to a single oval-shaped cell: “Moss cell”]

WARRING: Each consists of only a single layer of cells.

[One single leaf bit in the center is filled with green-ish cells.]

WARRING: These thin leaves can absorb water and nutrients directly from their surroundings,

[A stem of many moss leaves where the cells are still very large and visible through the microscope.]

WARRING: rather than having to transport water and nutrients from the soil through roots and shoots, like larger plants.

[A single tip of a moss leaf, with bumpy cells visible throughout. The very tip is transparent while the rest is green.]

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

[WARRING and TESSLER continue to look at the microscope through a phone video screen.]

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

[WARRING adjusts the portable microscope.]

TESSLER: Yeah.

WARRING: …and we’ll take a look.

[We are now looking at a single, bumpy layer of cells in the moss under the microscope. Each cell has a spindly point coming off of it.]

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

[A line points to one of these spindles coming off the cell: “projection”]

TESSLER: 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 and TESSLER look at the portable microscope through the phone screen.]

WARRING: Okay.

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

[The microscope focuses in on the transparent tip of a moss leaf, with little points coming out of each of the cells.]

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

[Another moss leaf under the microscope. The microscope changes focus to show small green-brown spheres on its exterior.]

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

[A line points to one of the green-brown spheres: “cyanobacterium”. The camera focuses a bit closer on the spheres. Then the camera cuts back to WARRING and TESSLER sitting on the rock in the forest.]

WARRING: 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 picks up a plastic vial with water in it and a pipette.]

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–

[WARRING dips the pipette into the vial of water and sucks some up.]

WARRING: –is to take a little bit of water–

[WARRING puts the tip of the pipette on the moss, squeezes the water out, then sucks it back in, and repeats this.]

WARRING: –and just kind of flush that water over the surface of the moss and pull it back up into this pipette and hopefully,

[WARRING puts a few drops of water from the pipette onto the microscope slide.]

WARRING: we will be able to trap some microbes.

[WARRING and TESSLER look at the microscope through the phone screen again.]

WARRING: Alright, so I can see lots of bacteria.

[We see a microscopic field of view with lots of little clumps of things scattered throughout the screen.]

WARRING: As the moss grows, it sheds dead cells, which are broken down by fungi and bacteria,

[A line points to a squirming and squiggling green rod-like organism: “bacterium”]

WARRING: over time forming a soil layer. This soil layer contains moisture and nutrients from the decomposed tissues, providing more habitat for more microbes.

[Microscopic close-up of a green microorganism. Text in the upper left side of the screen reads: “Cyanobacteria”]

WARRING: Cyanobacteria are here, too.

[Another cyanobacteria, looking slightly like sausage links filled with green cells.]

WARRING: These photosynthetic bacteria can play an important role in this community.

[Another cyanobacteria, two round circles filled with green squiggles.]

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

[WARRING and TESSLER crowd around the portable microscope.]

WARRING: Oh, here we go.. what’s this?

[View from the microscope. A small oval-shaped bacterium wiggles and dances on screen, its feather-like cilia on the outside just barely visible.]

TESSLER: Is that a ciliate?

[Text in the lower left: “ciliate”]

WARRING: That is a ciliate, yeah…

TESSLER: Oh, very cool

WARRING: A tiny wee one.

[A different ciliate, slightly fatter looking, moves around detritus and dirt bits.]

WARRING: Ciliates are single-celled predators that live by eating bacteria and other small microbes in the soil,

[A long skinny ciliate twists and turns through bits of dirt and small, non-moving bits.]

WARRING: this way contributing to the nutrient cycle. The diversity of ciliates we can find in this one patch of moss is astounding. Long ones,

[Another ciliate which is almost perfectly round, with a patch of ciliate on one end like hair.]

WARRING: round ones,

[A red oval-shaped ciliate eats small bits of other microorganisms.]

WARRING: red ones,

[A green fast-moving ciliate jets through a field of microscopic organisms and detritus.]

WARRING: and even green ones packed full of symbiotic algae.

[WARRING looks at the microscope and speaks to TESSLER.]

WARRING: 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.

[Microscopic organisms squirm and wiggle around the screen.]

WARRING: 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.

[A round organism with a tail at one end swims in a circle.]

WARRING: This animal is a rotifer.

[A different rotifer holds onto a brown piece of detritus with its tail while eating smaller organisms with its round mouth. A line indicates that the tail is actually a “foot”]

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

[Close-up of the mouth of the other end of the rotifer. Small hair-like cilia are pumping towards an opening. A line from the cilia reads “cilia”]

WARRING: At the other end is a crown of cilia that funnels water and particles through the mouth and mastax.

[Further down in the mouth is a structure that is opening and closing, almost like a throat. A line reads “mastax”.]

WARRING: The mastax is a simple pharynx that moves the incoming particles through to the stomach.

[A thin rod-like organism squirms around.]

[SQUEAKING]

[Lower left reads: “nematode”]

WARRING: 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.

[A puffy, elongated microscopic organism picks at a bit of algae with what look like claws.]

WARRING: One of the more charismatic microscopic animals is this one. This is the tardigrade,

[Text in the lower left: “tardigrade”]

WARRING: commonly known as the water bear or moss piglet.

[A different tardigrade wiggles around some algae.]

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

[A tardigrade in the center of the screen seems to walk in the water with its small legs.]

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

[A tardigrade wiggles past some algae using its legs.]

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

[A tardigrade eats a bit off of a clump of green cells near its head while it claws at the air with its legs.]

WARRING: 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.

[Camera glides across the length of a long thin nematode.]

WARRING: However, when the moss dries out, these microscopic animals can dry out, too. But like some of their larger relatives,

[A line points to an outer layer of the nematode. Text reads: “cuticle”]

WARRING: they possess a thick outer cuticle which serves to protect their soft bodies from fluctuations in temperature and moisture levels.

[WARRING appears back on screen speaking to TESSLER.]

WARRING: 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,

[Sped-up footage of moss tendrils growing.]

TESSLER: put a droplet of water on it and it will start photosynthesizing immediately after that.  

[A large mat of moss on a rock.]

WARRING: Together, the activity of the moss and the microbes forms a thriving, balanced community,

[Close-up of moss stalks.]

WARRING: one that can make the most of many environments.

[WARRING reappears, speaking to camera.]

WARRING: 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,

[WARRING and TESSLER pack up a box of equipment atop a picnic table in the Mohonk Preserve.]

WARRING: and use that DNA to help us identify what the different organisms are that make up this moss community.

[WARRING and TESSLER walk through the door of a laboratory. Text in the lower left reads: “American Museum of Natural History, New York City”]

TESSLER: Why thank you, Sally

WARRING: No problem

[Ziploc bags full of moss samples sit on top of a lab bench with labels of where they were taken.]

WARRING: 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.

[Close-up of hands on a microscope, and setting up a microscope slide. WARRING looks through the eyepiece of the microscope.]

WARRING: Some of this diversity we can see when we look through the microscope. But a lot of the time–

[WARRING is in the lab, speaking to camera.]

WARRING: –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.

[WARRING and TESSLER in the lab. WARRING opens a bag of moss with gloves.]

WARRING: Here’s moss number one.

[Gloved hands pull apart the moss, and put a section of it in a plastic bottle with water. WARRING shakes the bottle vigorously.]

TESSLER: Metabarcoding is this great technique where you can look at a uniform fragment of DNA across all the organisms in your sample–

[TESSLER reappears on screen talking to camera in the lab.]

TESSLER: –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 inspects the plastic bottle with the moss and water in it and shows it to TESSLER. They pour the water into a separate plastic cup.]

WARRING: Our process involves taking the moss and washing it through some sterile water.

[The plastic cup is attached to a hose, which attaches to a filtration machine.]

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.

[WARRING and TESSLER sit in the lab, speaking to each other.]

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.

[WARRING removes the filter, which looks almost like a coffee filter, from the filtration machine. The filter is covered in a brown layer. She places it in a petri dish and slices it with a razor into three pieces.]

WARRING: 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.

[The filter pieces are all put together into a plastic vial and shaken vigorously.]

WARRING: So, that filter gets taken and then put through a process to extract and concentrate DNA.

[WARRING holds up the vial at eye level and looks at it.]

WARRING: And it’s that DNA that we then send off for sequencing,

[WARRING opens a scientific fridge and puts the vial into it.]

WARRING: and then we get our sequences back and we can map them, as you said,

[WARRING speaks in the lab to TESSLER.]

WARRING: 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.

[WARRING and TESSLER pack samples of moss into a box.]

TESSLER: Shall we?

[They walk offscreen with the samples. Text reads: “This series was made possible with a grant from Science Sandbox, an initiative of the Simons Foundation, and with the support of the Gordon and Betty Moore Foundation.”]

[Credits roll. While they roll, WARRING’s voice is heard offscreen as she and TESSLER walk through the lab.]

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 meta-barcording, expand our ability to explore our planet’s extraordinary microbial diversity.

[Microscopic footage was recorded at AMNH on an upright benchtop microscope.

Created by Sally Warring

Executive Producers
Erin Chapman
Eugenia Levenson

Associate Producer
Lisa Rifkind

Cinematography
Serena Kuo

Microbial Footage
Sally Warring

Editor
Serena Kuo

Animation & Titles
Ramin Rahni

Color
Serena Kuo

Original Music
Ramin Rahni

Location Sound
Jon Flores

Studio Sound
Russ Baird
Jesse Vance

Narration
Sally Warring

Sound Mixing
Jon Flores

Special Thanks
Sara Bender
Greg Boustead
Du Cheng
Daniel Smiley Research Center
Keith Dunning
Mohammad Faiz
Rhea Gordon
Jessica Harrop
Adam Jones
Jon Kaye
Eunsoo Kim
Janine Luke
Elizabeth Long
Mohonk Preserve
Sam Riviello
Mark Siddall
Emily Summerhays
Michael Tessler
John Tracey
Arthur Warring]

[END MUSIC]