Week 4: The unseen world

Let's get a feel for what we mean in this international year of biodiversity, just what we mean by biodiversity, the sheer scale of it.

Yeah. Biodiversity is a wonderful term, because it takes something that's extraordinarily broad and focuses it into a single word. And really, what that word represents is all life on Earth and its variety. When people who have heard the term before - heard the term biodiversity - they tend to conjure images of individual species, like lions and tigers and bears. But really, it's much bigger than that. It includes the smallest life forms, the microbial world, on up to the largest creatures on the planet. But importantly, it also includes the diversity of communities they form. And scientists call these things ecosystems. But that is also another important form of biodiversity.

The sheer scale of this unseen, the microworlds of biodiversity, actually baffles me. Have we got any idea about how immense it is? Or is it impossible to quantify?

Well, we know it's immense enough such that the diversity of genes in the microbial world - we know that that is far greater than the diversity of genes in the rest of the living world. But really, we're utterly ignorant about the microbial world. In fact, it is the last great unexplored frontier in life on Earth. And just in the recent past have we started exploring it with any amount of force.

Well, I read something the other day that said there was something like in 30 grammes of soil in a Norwegian conifer forest, there was something like 500,000 species estimated of microbes or bacteria, including everything. How on earth could we possibly grapple with sort of figures?

That's a good question. The wonder of the microbial world is that it continues to redefine our understanding of life. We, as large creatures in the scheme of life, tend to think that species are other large things. And so when we think about the microbial world, we try and put these concepts of what life forms are onto these small organisms. And it turns out that identifying even a species of a microbe is a rather challenging task, because microbes, it turns out are quite promiscuous. And they swapped genetic material all the time. In fact, it may come as a shock to some people listening to this programme that in fact, there are significant portions of our own genes that come from microbes. And they have, over time, managed to get their genes into us. But the diversity in the microbial world of the genes is profound, and not just in terms of the awe that one gets when considering how much diversity is, but also in terms of its relevance to human well being.

Well, you've touched on how it affects us. I just want to go back to what you were saying, then, about species concepts. We know when a blackbird or a robin is a blackbird or a robin. What about microbes? Are they continually changing? Can we put them in species boxes in the same way that we often do with larger animals?

Right. It's proven that the definitions we've used to define species of big organisms just don't seem to fit very well for the microbial world. We have these definitions of species that are based upon appearance for species. So if one organism looks like another organism, that might mean they're the same species. We also use definitions based upon reproduction - so if two species are capable of mating and producing fertile offspring. But really, those definitions don't work hardly at all in the microbial world, because of course, most microbes don't have sex, or at least not in the way most people would consider it. And they oftentimes will look very similar under a microscope, and yet their genetic material is profoundly different. So it's been a great challenge to biologists to come up with meaningful definitions of essentially what would be a species in the microbial world. And really, there's still an ongoing debate as to how best to do that .

So they're not playing it by the rules we already know and the rules we attach to larger organisms. But are they changing as well? Is there evidence that, as well as not necessarily playing by those rules, they're also evolving as we observe them?

Absolutely. There's some fundamentally different biological processes that occur in the microbes of the world than in higher organisms. And some of those different processes allow them to change much more deftly than higher organisms. And that really gets down to the most molecular level. The machines that they use that copy their genomes are much less accurate than those in higher organisms. And so their rates of mutation in their genomes tend to be much higher. And that enables them to adapt to new environmental circumstances. I see this as a doctor all the time in antibiotic resistance. So there are bacteria that infect humans which have become resistant to many different antibiotics. One of the most widely known is methicillan-resistant staph. aureus, or MRSA. The bacteria is called Staphylococcus aureus. Methicillin is an antibiotic class. It's a group of antibiotics or defines a group of antibiotics that used to readily kill this bacteria. But because the bacteria evolve so quickly under pressure - under pressure, in this case, from antibiotics - there are some of them that have mutated to become resistant to this antibiotic. And so as a paediatrician, when I take care of children, this has become a major issue for our ability to treat what used to be a really rather easy, treatable bacteria. But of course, this ability to change their genomes has had enormous influence in other ways. There's another bacteria that lives in hot springs called Thermus aquaticus. It was originally discovered in the Yellowstone National Park in the United States, living at about 70 or so degrees Celsius. That's a temperature that would cook us alive, but these bacteria call it home. And they're able to do that because the copy machine they use to replicate their genome works just fine at that temperature. In fact, that's near its optimal temperature. And that machine produced by that bacteria is the basis for a diagnostic test called the polymerase chain reaction. It's the basis of all of these crime show lab scenes in which they're trying to sort out who the criminal is. And they use this technology called PCR, polymerase chain reaction, to identify criminals. We use it to test for infectious diseases. It has been described as the single greatest discovery in biology of the 20th century. And this is all because of this bacteria's ability to adjust its ability to live based upon evolution and its ability to change its genome.

I want to move on a little bit now just to talk about diseases that occur, things that come in from the outside. We've talked about heritable microbes. What about the proportion of disease and microbes that affect us that have a life cycle outside people? Because the more we change their world, then, and the more we change the world outside us, surely the more vulnerable we are to receiving infections from those pathogens, from those creatures. Can you talk a little bit about that?

Sure. I hope everyone's sitting down, because it turns out that while we like to believe that when we get sick, we caught it from our work colleague or from our child or from someone we sat next to on the train, it turns out that although the source of that illness to us is most often from another person, a majority of microbes that cause disease in humans in fact have life cycles that, as you point out, include species other than ourselves. In fact, if you look at the 1,400 or so known pathogens of humans, probably 60% to 70% or so fall in that category. But what's interesting is that the new pathogens, the so-called emerging infectious diseases - these include both diseases that we've known for a long time such as tuberculosis that are spreading around the world, but also entirely novel microbes, such as SARS or the H1N1 virus. If you look at so-called emerging infectious diseases, that percentage gets even higher. And it raises the question as to whether changes to ecology on a much grander scale, as you point out - ecosystems around the earth - may be playing a role in disease emergence. And there's certainly evidence to suggest that, particularly with SARS, for example, but also with other emerging infections-- that because these microbes inhabit organisms that are not humans, that changes to the ecosystems that those organisms live in may in fact cause them to change where they live, and in some cases, that leads them to move into humans, where they had not been in the past.

So an example for that, for example, something like H5N1, which was caused by the proximity of poultry or birds to us?

That's right. So the flu virus, people refer to H1N1 as the swine flu and H5N1 as the bird flu. Well, it turns out that flu viruses infect lots of different organisms. And they tend to actually be like first cousins. So what distinguishes a swine flu from a bird flu from a human flu is really which organism the virus infects best; which of course, has to do with the genes within that virus. But as I was mentioning, with microbes, and particularly with viruses, their genomes mutate quite readily. And so when their genome is able to mutate and change, it changes the potential with which they may infect a different species. This is exactly what happened with H1N1. The flu virus has eight strips of genetic material in it. And the H1N1 virus, in order to make it be capable of infecting humans, swapped out one of those eight segments. And that new segment of its genome, essentially, was the trigger that enabled it to move. Now, where exactly that got introduced and how it got introduced is shrouded in mystery at this point. But we know from past flu pandemics that the flu virus swaps pieces of its genome in and out among pigs and ducks and humans and other creatures that happened to be put in close proximity. So it would not surprise me at all that the event that led to this new flu emergence was due to some concurrent exposure of multiple species to this virus that enabled two different varieties of the virus to get very close to each other and swap their genetic material.

So the message from us is that we're not separate from the natural world. We're not separate from ecosystems out there. We're part of them, and we either pay the penalty or reap the reward, depending on how closely involved we are and how we modify those.

Right. The image I like to think of when it comes to our relationship to nature is that really, the entire living world, including us, is like a tapestry, and that we are as enmeshed in that tapestry as any other organism. And as you're well aware, the amount of biodiversity on Earth at present is declining at a rather impressive and alarmingly impressive rate. And so this tapestry is essentially getting strands yanked out of it. And we are trying our best to shine flashlights on various corners of this tapestry to understand our relationship to it. But really, we don't understand it very well at all. And so we don't know which strands that get pulled out are going to affect us, nor do we really understand the composition as a whole, because we only are able to glance at various small pieces of it. And as much as we try to pull ourselves out of this tapestry to make ourselves believe that we're independent of nature, nature is continuously pulling us back into it and reminding us-- through these outbreaks of infectious disease, through our difficulties with supplying food, through the antimicrobial resistant problem. We try and convince ourselves, kid ourselves that we can live apart from nature. And yet, the more we do that and the more we act in that way by degrading ecosystems, decreasing natural habitats, influencing the global climate, the stresses upon the fabric of life yank us back to it.