The fascinating lives of microbes | Alex Penn | TEDxSouthamptonUniversity


Translator: Ilze Garda
Reviewer: Reiko Bovee So, hello. I’m here to talk to you today about interacting
with microbial communities. So, when you think about microbes,
if you do, you may think of something like this: single species of bacteria or fungi growing in a Petri dish in a laboratory. But the way the microorganisms
live in the real world, couldn’t be further from this. Microorganisms are living in complex, multi-species communities, and the vast majority of these species are really as yet uncharacterized. We can’t even grow them in a lab. They are in every ecosystem on the Earth. You, yourself, are a bacterial ecosystem. There are ten times as many
bacterial cells in your body as there are human cells, and a hundred bacterial genes for every one of your genes. Bacteria and other microorganisms
are crucial players in all terrestrial and aquatic ecosystems, those we rely on for our survival. And soil is a great example of this. So, in just one teaspoon of soil, you are likely to find more individual bacteria than there are human beings on Earth. And there are debates raging about the number of species, the species diversity in soil. Estimates range from something like 100,000 species per gram to 16,000,000 million species per gram — a huge number, far more species than there are species of mammals. And these sorts of bacteria, they’re not just passively
sitting there next to each other. They are engaged in complex interactions. And these interactions provide nutrients which we need. So, nitrogen, for example — all of the naturally occurring
bioavailable nitrogen, which plants need for their growth, is fixed from the atmosphere by the action of bacteria, these bacteria are either living
in association with the roots of plants or freely living in the soil. The other alternative to this, of course, is energy-intensive fertilizer production. But really without these bacteria, there would’ve been no plant ecosystems. Fungi also play important roles in terrestrial ecosystems. Phosphates are also vital
for plant growth, and mycorrhizal fungi form connections with plant roots in the soil, forming vast networks of fungal roots. They’re bringing phosphates to the plants in return for sugar from photosynthesis for their metabolism. Not only that, they provide protection from pathogens, protection from drought stress, all sorts of other benefits. This is a very ancient symbiosis,
an ancient relationship, and this, in fact, may be the way in which plants first made it onto land by associating with fungi. In short, microorganisms form the backbone of planetary metabolism that implicated in everything
that is cycling around. Not only are they bringing down inorganic minerals from the atmosphere
and up from the rocks, they’re cycling these things round once they get into the ecosystem by decomposing the bodies of dead organisms. Twenty percent of the oxygen
in our atmosphere is produced by cyanobacteria living in the oceans. And on a longer timescale, the chloroplasts in plant cells that allow them to photosynthesize were originally free-living bacteria. So, it’s absolutely true to say that without bacteria we would not
have an oxygen atmosphere. So, it’s clear that we depend on these ecosystems, and on these microorganisms. But it’s also crucial to know that we interact with them very strongly. So, what we do to the environment, drives the community composition, drives the evolution of microorganisms. For example, in soil, agriculture, ploughing, putting on fertilizer changes what’s in the soil beneath it. And we often don’t know how these microbial ecosystems will react to the kind of interventions that we make. We’re really currently performing several vast, blind experiments in microbial interaction. So, for example, antimicrobial’s being
pumped into soils, from manure from intensive farming. Or, of course, the very big experiment of climate change. Changing weather patterns, particularly precipitation
and carbon dioxide levels, will certainly vastly change the community composition and drive the evolution
of microbial ecosystems in ways which we can’t yet predict. So, this kind of interaction happens even on a very small scale. You, yourself, in your own garden, if you water the soil,
you put compost on the soil, you’ll be changing
what’s there in the soil, changing the composition
of these ecosystems. Effectively, you’re a member
of these microbial ecosystems. And not only is this
really important to understand, it’s also really amazing,
I think, it’s really exciting. And we wanted to find a way to make this visible to everyone. The question was really how to do it. So, microbiology is normally done by scientists with specialized equipment, and there can be some rather constraining health and safety considerations to take into account. So, we needed to find
a different way to do microbiology, to take it out into the public domain. We set up a project,
called Community Microbes. And basically what we did was to develop “kitchen sink methodologies,” for microbiology: simple protocols that could be performed by anyone without very much specialist equipment, media for growing up bacteria which would… from
supermarket shelves essentially, Horlicks, marmelade, honey, and came up with protocols for people to look at their soil ecosystems. So, the idea was that people
would take soil samples from their gardens, of anywhere that interested them, from different points in these sites, in which different sorts of interventions might be taking place. So there was compost there, or someone had planted some mycelias, or what have you. We’d helped them
to culture up these bacteria and then compare what was present in these different parts of the ecosystem. So, we’ve been running these experiments with all sorts of different people, all of them non-specialist, and in a wide variety of different sorts of environments. So, classrooms, yards, here — very windy polytunnel. And, as you can see,
we’ve got quite low-tech conditions; we were running this experiment outside, we’ve even had to use black bin bags here to create a clean surface on which to do the experiments. And what you can see in this photo, is people have taken soil samples, they’ve come up with hypotheses about the interventions which might be happening, taken their samples, and they are putting the soil, a few grams of soil, into some water, and then taking a bit of water from the suspension and plating it up on a Petri dish with simple aseptic technique. Then we take the Petri dishes
back to the lab and incubate them. And then we are able
to bring them back again, so that people can then see what grew up in the different places that they sampled from, try to understand what’s happening with these different ecosystems, due to different sorts of human intervention. And it’s really been a fantastic opportunity for people to really
look closely at the ecosystems that are right there under their feet. So, these are some of the sorts of things
that people were producing. And you can see from
just a very normal soil sample, you get quite a huge variety of different sources of bacterial species, all sorts of lovely forms and shapes. You can see some
sort of look a bit like seaweeds, some that are filamentous, and here, we already start to see bacterial interactions. So, on the bottom right there, you can see there’s a colony that has gotten
an exclusion zone around it. It’s producing an anti-microbial to suppress the growth of other species. So, we see a lot’s going on, even in just these very,
very simple experiments. And, these really are quite beautiful things, it’s quite– I think people have found it fascinating to just take a few grams of soil and then to be able to delve
into these sort of hidden microbial worlds that are right there. They can unveil it themselves. They can do the experiments themselves. And it’s exciting for us, too, because — I mean, really, every time you do this, you see a new species, you see something unexpected that you haven’t seen before. And they are just…
they’re very beautiful objects. So, these experiments have been very successful at showing species diversity and how it correlates
with human interaction. But if we want to understand how we intervene with
these systems in more detail, we really need to look at the interaction between the bacteria themselves. So, we wanted to take
this idea out on the road, and get people interested in bacterial interaction. So what better way to do this,
we thought, than creating a giant Petri dish and inoculating it with
different bacterial species? So, we’ve set this system going, it’s about a metre across, with lots of different species of bacteria, naturally coloured, all that are quite well characterized. This is a system developed
by Dr. Simon Park. And we’ve just let them grow and interact, essentially, playing a giant game of microbial risk. And what you can see here, is that the red is the kind
of winning invader. It’s taken over most of the space. But you can also start to see
there are more sophisticated interactions: exclusion zones I mentioned before, around the different types of bacteria where they’re suppresing each other, and interesting kinds of
synergistic effects. But even in this very simple system, in which we understand
all the bacteria a priori, we know everything that’s in there, we get unexpected effects. These comet’s tails, for example, around the orange colonies, we don’t know why they are growing
or what’s happening. So, we’ve really got a long way to go in understanding bacterial ecosystems, their diversity, the interactions within them and our interactions with them. But we really need
to understand these systems. As the century goes on, we drive them and push them harder more and more so. But we need a radical change
in perspective in order to develop this understanding, because we are members
of these ecosystems. And the reality is we are not just passive observers looking down on the game. We are right there in the Petri dish with them. Thank you. (Applause)

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