Conservation of Microbes

28 October 2012

Interview with

Dr Gareth Griffith, Aberystwyth University

Microorganisms like bacteria are absolutely everywhere.  We've yet to investigate an environment on Earth that hasn't shown at least some evidence of bacteria life. 

Even their ubiquity and their ability to survive in almost any environment as well as their reputation for causing diseases in humans and in important crop plants, you could be forgiven for thinking that microbes are not, and should not be, a conservation priority. 

But that's not the case according to Aberystwyth University researcher Gareth Griffith.  He's calling for a global strategy on microbial conservation and he joins us now.

Ben - So Gareth, microbes, are they really under threat?

E. coli bacteriaGareth -   Certainly, we need to change the perception that they are everywhere and all of them are everywhere, and therefore, by definition, they're unlikely to be endangered, or go extinct.  That was a perception that held strongly for a long time in microbiology.

Ben -   This was the strange idea that essentially, all microbes exist everywhere, but the environment then just selects out the ones that succeeds.  That's not the case, you're saying.

Gareth -   No, there's vast amounts of evidence now.  As we look more closely, that is not the case.  Most species that have been looked at show biogeographical distribution.

Ben -   So, with regards of conservation, what actually is the problem that we're facing?

Gareth -   I think in the case of the microbes is that, it's the absence of any appreciation that they might face extinction to start with.  We're starting at the very bottom here.  It's not that they're neglected.  They're not even considered.  I don't think the CBD (Convention on Biological Diversity) has made any mention of bacteria or the archaea in terms of the fact that they might be threatened.  I'd extend it just to point out that all of these domains of life, all of the kingdoms within the eukaryotes, the ones we focus our attention on are just the two kingdoms of plants and the animals, and all other ones need some attention.

Ben -   So, they're not appearing on the Red list.  They're obviously not becoming icons for animal preservation societies.  How is this reflected in the actual scientific research?  Is there a body of mainstream conservation research into microbes that just isn't getting the promotion, or is the research not there in the first place?

Gareth -   Well, some microbes are getting some attention.  I'm a mycologist.  That's my specialty within microbiology and some fungi are attracting some conservation attention, but definitely second class citizens relative to the plants.

Ben -   We know that some fungi actually play incredibly important roles in keeping plants alive.  There are what's called mycorrhizal relationships between the roots and the fungi that live in the soil.  Is this the sort of thing you were worried about losing if we fail to conserve microbes properly?

Gareth -   Yes, the survival of many larger organisms is very likely dependent on the presence of certain microbes that help them function properly.

Salmonella bacteriaBen -   So, it isn't just the case that we need to conserve them for their own sake, but in fact, there are various knock-on effects that we could have if we fail to put this effort in.

Gareth -   Yes, I think we're learning an awful lot now.  The fact that we can do this next generation sequencing, this very high throughput sequencing now is revealing to us where these microbes are and also where they aren't.  And also, for example in human health, the fact that the vast majority of gut microbes aren't pathogenic to us.  We're now building up a picture that the absence of a healthy gut community leads to ill health.

Ben -  
In fact, we'll be hearing a bit later on in the show about how a certain cocktail of gut microbes can help protect against C. diff which is a very dangerous infection.  So, does that mean that there's a genetic wealth of potential out there in the microbial community that we could be taking advantage of?

Gareth -   Yes, if you take it as a whole, the microbes are metabolically hugely diverse and can conduct many biochemical reactions that animals and plants can't conduct.  Therefore, for our own sake, just for biotechnological reasons, we have an interest in making sure that none of them go extinct.

Ben -   That reflects something that a user on Twitter said, their name is FoodiFanciPants.  They've got in touch to say that parasites and bacteria are nature's unique chemical converters, and so, they're absolutely worth conserving.  Now this seems quite a one-sided way of looking at it.  We think of things we can do with them, things we can use them for, opportunities we have to exploit them.  Presumably, there are also broader arguments with regards to the fact that these are just as worth conserving as any panda or rhino?

Gareth -   Yes, all species have equal value in that respect.  I know that some will attract more attention, like the panda, but there's no reason to have a hierarchy of importance amongst the organisms that inhabit the planet.

Ben -   So, what do we now need to do to start - not just actually start conserving them, but how do we select priorities amongst microbes because we have our Red lists that categorise things as critically endangered or endangered, or extinct in the wild.  That gives us a hierarchy of priority as to which ones need the most efforts.  How can we start putting together something like that for species as diverse and as poorly understood as the microbial community?

Gareth -   I think
exactly as Simon said earlier.  We need to focus on the habitats, but not just the habitats where you can see larger organisms.  There's virtually no habitat on the planet that is sterile, but there are many that don't have macroorganisms, macrobes as I think of them - all the animals and plants that are visible.  So you could take the hot springs or the many cold areas of the planet where there aren't any larger organisms, but there are diverse microbes present there.  So it's concentrating on habitats, but not just all habitats.

Ben -   One habitat that you have mentioned in some of your writing about this is actually Lake Vostok.  This is an interesting subglacial lake which we know that a Russian team have been attempting to make their way down into.  Presumably, it could harbour unique microbial species.  Is this something we need to think about before we actually get into that, just as much as we think about making sure we don't accidentally infect Mars with microbes on space probes?

Gareth -   Yes, I think it's an excellent argument.  With Lake Vostok, since I wrote the article that we're talking about, the Russians have drilled in, but I think they did face quite a lot of criticisms so they were more cautious than they had originally intended to be.  So they only actually extracted a small amount of water and didn't find anything in there.  But I think their next attempt will involve a lot more caution because of the dangers of infecting with surface microbes.

Ben -   Speaking of infection of course, the one thing that really makes people think of bacteria and microbes is in their role in human infection and in destroying plants.  How can we balance the need to conserve these sorts of species with the fact that actually they're deleterious for our health or our lifestyles?

Gareth -   I think in many cases, and I think C. diff might be a good example of this, it's the disruption of healthy natural microbial ecosystem that can lead to disease.  Nature abhors a vacuum therefore, if you disrupt the existing ecosystem, pathogenic organisms can thrive.

Ben -   You're calling for what you've called a global strategy for microbial conservation.  How would that actually work?

Gareth -   I think it's up to us as microbiologists to get ourselves together and decide to focus on certain priorities.  As I said, it's those habitats that are neglected, they're the ones that the microbiologist could focus on.  The one I haven't mentioned yet is soil.  Soil is tremendously important for all human activity yet, very much unknown.  We know that they're most diverse habitats on the planet, even Leonardo da Vinci 4 or 500 years ago said that we knew more about the stellar constellations than the soil beneath our feet, and that is still true now.

Ben -   So, there is clearly a need to try to conserve these habitats.  What sorts of scientific techniques are we actually able to put to the task?

Gareth -   We're very lucky to be benefiting from advances in molecular biology, especially high throughput sequencing.  This is the technique that will shortly give us the one thousand pound human genome and so forth.  These things can be applied to the study of microbial ecology as well.  So we can just take samples of seawater and sequence all the organisms in them, metagenomic studies.

Ben -   So, this allows us to see all of the different genes that are there to work out all of the different species that might be hanging about, and that gives us a really good idea of where our priorities need to be put.

Gareth -   Yes.

Ben -   Well, thank you very much Gareth.  That is Gareth Griffith from Aberystwyth University.

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