Learning from nature how to eliminate livestock methane emissions with Prof Athol Klieve - University of Queensland

Could nature provide a map to greatly reduce the climate impact of animal agriculture. Dr Athol Klieve has spent his career researching the microbiome of ruminants and kangaroos and why ruminants produce methane and kangaroos do not. In our conversation Athol also explains how there are no identifiable patterns in nature as to why a particular species produces methane or does not produce methane and that with us humans, some of us produce methane and some of us don’t. The exciting thing is that the current situation is not fixed, things can be changed. 

Athol also delves deeply into the complex community structures within the microbiome, how micro organisms cooperate with each other, how they compete, how they protect or sabotage other microbes and, how they communicate or talk to each other. He also discussed the adaptability of microbes to change their metabolism and even genetic pathways under different conditions. The ultimate focus of Athol’s research has been how to better understand these complex ecosystems to improve animal agriculture and drastically reduce livestock methane emissions. 
 
I recently caught up with Athol to hear more about his work.

Transcript

AS

Good morning, Athol. And thank you very much for joining me today. Could we just start with the background of how you got into researching the microbiome, ruminants and other species? 

AK

Well, I guess the whole point about animal agriculture and trying to improve animal agriculture in the ruminant space is that those animals are entirely dependent on the biome that their microbiome in the gut, and in particular, the rumen microbiome for virtually all of their energy and protein requirements. So it's a necessity to know and understand how the microbiome in those animals works. And indeed, as we're finding out more and more how the microbiome in all animals works. And if we're looking at finding ways of being able to keep costs down of production and improve productivity, for a world that's needing more and more animal protein, then understanding the microbiome and how it works and trying to tinker with it to improve it is the direction to go with and that's where that's where we came into our interests came into it.

AS

So you started researching ruminant nutrition, microbiome back in at the University of New England in Australia, do you want to just give us a be a brief background into what processes what tools and techniques you had when he started off, and then how that evolved in terms of, were there any more tools or different ways of looking at the systems?

Unknown 1:59

Well, that's a massively big question. And it really goes through a complete revolution in in our area of science go through that period. When I first started at UNE working in this area, this would have been the early 80s 1980s And basically, techniques were based on the ability to cultivate and grow the microorganisms in culture, so using classical microbiological techniques. So all of our knowledge on the microbiome and how it work was based on the organisms that we could grow in the lab, be they bacteria, fungi, protozoa and in my particular case I had a speciality in the area of bacterial viruses. But the thing was at around that stage, molecular biology was just starting to Virgin and just starting to come into its own. And with molecular biology, we had the ability to extract DNA from everything that was actually in the gut microbiome and initially there was some there was a lot of DNA DNA hybridization used, and what are called clone libraries where you take the DNA and you have a shotgun clone library, and that way you could actually you can actually see what you didn't know, in many ways, and that's where we found that up to 90% of the microbes, in particular, the bacteria. And the Archaea that were living in these micro biomes in the rumen, weren't actually the ones in culture. And so we then had to have a major rethink about what we understood about the whole ecosystem. And we actually worked out that we didn't know how or what to do the truth. And from there, Polymerase Chain Reaction came around PCR and then there was also gone from the very original DNA sequencing techniques, Sanger sequencing techniques, which were long and laborious. I know a particular PhD student who spent his entire PhD sequencing about to kilo base pairs. of DNA. That was his entire thesis to the high throughput type DNA sequencing technologies that we now have, and and then moving from there. And that was able to show us what was actually there in terms of the organisms that are present that did help us actually get some more organisms into culture as well. So we could work out what they did, how important they were, and also showed us that a lot of the microbes that were dominant weren't necessarily ones that we had in culture. And that is now moved on to even to transcriptomics. So we can actually work out not only what organisms are there, but which ones are active, which ones are actively metabolizing materials that are there. And then we end that proteomics and metabolomics and all the other omics type studies and sciences that are now available to look into what microbes are there, what they do, what they produce, and how they produce things. So it's moved along a huge amount during that period of time. And it still continues to move along. Great pace at the current time.

AS

In many ways, that sounds a bit like you know, if you're looking at just biology and suddenly you using your naked eyes, and then suddenly you've got a microscope, and it's such a huge step change. It must have been a very exciting time to be researching as all these new windows into life and how it works came about.

AK

Yes, absolutely. It did. It did. It went from time so thinking that we knew quite a lot about something to find out that we actually knew very little about something because all the new information that we got, was teaching us just how much we actually didn't really know and how much there was to find out about what was happening in them what was going on. And even the use of stable isotopes to detect, for example, where metabolites went to what was using those metabolites and where it went to so for example, if you were able to grow a plant with carbon 13 in it and then you put that into an ecosystem, the first things that could break down those plant tissues would have the carbon 13 Turn up in their DNA, the earliest and so you could work out what things were using the foodstuffs that we're giving him.

AS

Well, that's, that's, that's amazing. One, I guess this question is a bit how long is a piece of string so I know that's a bad question to give to a scientist. But you said that we went from thinking we knew a lot to thinking we didn't know very much at all. Where'd you see that? Where do you see us now in terms of how much we still have to know compared to what we do know?

AK

Yes, that is a bit more like a piece of string. Basically, we know a hell of a lot more. We know a lot more basic information. But we're also learning that we also need to know things that we hadn't realized before, like how organisms communicate with each other, how they cooperate with each other when they for example, using metabolites and the like. We actually getting knowledge that these particular in any complex ecosystem, a lot of these things if you like to use the terminology talk to each other. They they synchronized. There's also a lot of competition going on between them as well. And and we need to understand that because if we're looking in an ag from an agricultural perspective, as opposed to a natural ecosystem perspective what we're trying to do is to direct the metabolism in such a way as to maximize the efficiency for what we want, which is the efficiency of, say degradation of plant fibre, for example. It's not saying that the that the process is inefficient as it is, but for our particular targets or goals in this area. If we can manipulate those to reduce some of what we would call inefficiencies and promote the direction that we're going. That's basically what we're trying to understand. So our ability to understand everything in such an incredibly complex system is probably still a fair way off, but to understand enough about aspects of the system to be able to improve it in the direction we want to improve is well within our reach.

AS

That's very exciting to hear, I think in some of the other with some of the other people I've spoken to, and they've alluded to what you said about the microbes communicating and actually collaborating with each other. I see. You know, from my perspective, I see that as an opportunity to if there are communication signals, that's an opportunity where you can actually intervene potentially. Because the balance, what I see is there but also how its operating. How do you how do you see that that balance?

AK

As in which terms the balance

AS

What’s more important having the species in the rumen and or present or how they are actually interacting and collaborating?

AK

It's a good question, because I think it's how they're interacting and collaborating. There's a lot of what would you call it? inbuilt redundancies in the organisms that are present and what they do? So basically, if you for example, you might have a dozen different strains of a certain species, if you knock out a number of those others can take over that particular role in terms of the you know, the specific breakdown of certain products and use of certain substrates that they do. But it's how they communicate with each other and the effectiveness with which they do it. You might have for example, an organism that is dominant because it's able to out compete other organisms, but it only breaks down it only breaks down the material quite slowly. So break down cellulose quite slowly. Whereas if you could influence another particular species that breaks down quickly but isn't as competitive to become more competitive, then then you would be getting an advantage coming through then.

AS

in higher organisms. Metabolism changes with age it changes with levels of stress, it changes with temperature, humidity, etc. How are our microbes affected? By the age of the microbe or the levels of stress? They're under does that change their metabolism? Or is that something we even know?

AK

It’s both absolutely, and we don't necessarily know it's it certainly it certainly is now the age of organisms. It's interesting point. Given that, you know, organisms reproduce by binary fission, so you know, they're splitting in half and then you got two new cells, but it has been shown that some older cells and some older cells will die. Actually do change their metabolism, but they also change their metabolism, with temperature with metabolites present with osmolarity with just about everything that you can think of, but the really interesting one is also they will change their metabolism some of them with a rate of growth. And the rate of growth as affected by say wash out from the rumen or what or whatever it is, or the amount of substrate that's available to them, can affect markedly the type of products that they produce, they can actually even switch to different to different genetic pathways at different rates of growth. A really good example of that, that we have seen and we did some work on this in Illinois back in 2014 was with streptococcus Bovis, which is a known lactic acid fermenter and lactic acid reducer sorry, it's always been a problem, but it's growing really, really fast. So the animals just gone onto a grain diet. It will produce just about pure lactic acid. It's a homo lactic producer. But if you get back to an animal that's on a forage diet, the strep bovis populations are actually about the same. They don't really increase that much unless the animal goes acidotic, then they go up the roof, but the difference is that they produce very little lactic acid. They produce other metabolites, acetic acid, bit of propionic and some others as well, so you can change that. But the other the other big interesting thing that we're only just getting a hand on and this is really the whole whole of animal biome, if you like is the interaction between the animal itself, the physiology and the animal, which as you rightfully said will change with all sorts of different things, but that also interects directly with the microbes, so directly through salivary inputs, through materials coming in through the rumen wall etc probably temperature changes, all sorts of other metabolite changes and we don't really understand how that interaction occurs. And what we can do about that. There's also the genetics of the animal genetics of the animal appear to have an impact on the type of microbes that are able to colonize the gut as well. And that would be another area that would be particularly of interest to understand how that occurs.

AS

At some stage through your career, you started looking not just at ruminants, cattle and sheep but at other species. Do you want to just tell us a bit about that,

AK

he's really, really, I mean, the major other speech, we did look around at some other species just from the point of view of interest in what type of microbiome they had but the major ones that we're really talking about here at kangaroos. And really, that goes back to the whole methane issue. So basically, when we're looking at improving the efficiency of the microbiome in the rumen and metabolism, the big inefficient one that sticks out, is the production of methane. Methane is energy rich. If the if instead of producing methane, we could channel the substrates that produce that into other usable substrates and the obvious one here is a process called reductive acetogenesis. We're acetate is produced which is a major VFA that's used for energy by the animal. Okay, so it came to our interest and it was all from the from the foregut fermentation. So from the ruminant perspective, that while ruminants lose anything up to about 10 to 14% of the entire energy that they produce in methane going out to the atmosphere. Other animals that have what is apparently a similar type of digestion it’s not the same, because those animals did evolve entirely separately. But the thing is that the macropod, kangaroos have a foregut fermentation that functions is functionally similar to the rumen. It's it's a huge chamber that microbial activity breaks down forage breaks down plant material, to produce VFAs. And the material flows through then into the true gut where the microbes, etc are digested, and that produce the protein for the animal. So that's the same sort of system but the interesting thing was that had been reported back probably in the late 60s 70s That 1970s That kangaroos, particularly the larger kangaroos didn't produce methane. And so that is really what fueled our interest in looking into other animals. Is why that happened. And if that happens in a foregut fermenting animal that feeds on pasture, and often with the grazing kangaroos, the very same pastures that cattle and sheep are feeding on, then, is it possible to get a similar or to be able to move the microbiome in sheep and cattle to a situation where they can do a similar thing, and therefore that 10 to 14% energy instead of going out in the atmosphere and causing or contributing to issues that we have with with global warming and climate change. If we could channel that through into, you know, growth, improve growth, then we'd be getting a lot more meat or milk available from those animals. Without any extra feed being required. And that's where we that that was really our driving point to look at kangaroos.

AS

So where, I guess where's that at and what would be the next steps there?

AK

Well, we, we finished when I finished at a point there, where we were able to introduce stable isotope probing or stable isotope tracing, and we were able to show definitively that the precursors of methane which is carbon dioxide and hydrogen, in cattle, the stable carbon goes into methane as you would expect out that way. But it in kangaroos, it ends up in acetate, and so we were able to actually show that the predominant method for a removing hydrogen, in particular from the fermentation in kangaroos is reductive acetogenesis, and we're able to then go through and we were able to isolate, I think two or three species of reductive acetogens that utilize carbon dioxide and hydrogen very efficiently indeed. And they weren't known species that hadn't been cultured before. But we're also able to show that that was basically the tip of the iceberg, and that there were a whole range of other bacterial species in kangaroos that were basically reductively acetogenic. So there are forming acetate from hydrogen and carbon dioxide. So, where we were thinking of looking at well, there's two approaches. One is the hopefully we might be able to isolate those microbes, and hopefully, they might be able to colonize or persist in ruminants. Now, that was probably a long shot on its own, but it's probably worth having a go. The other thing is to try to understand what conditions or what sort of circumstances or what other microbes are required to enable them to dominate in say the kangaroo forgot, when they when they don't dominate in in the rumen and they do occur in the rumen, they don’t dominate. Yeah, so that's where the directions and the direction the main direction we're interested in was to understand how that can happen and kangaroos so that we might be able to emulate similar system, similar circumstances in the rumen and to generate that advantage to the reductive acetogens.

AS

So that goes back to understanding how those, the interactions between those bacteria and the other bacteria that are present plus any potential communication molecules or signaling molecules or systems that turn them on or turn them off or tweak their metabolism.

AK

Yeah, yeah. And it may it may be more complicated than that, because it might be that there are certain microbes that actually protect them. In that situation as well. So you might have ones that they work in synergy with, but also ones that are able to be antagonistic to say methanogens and that type of thing in the in the rumen as well. And and we have to remember  it's not the only ecosystem were the only fermentative ecosystem where reductive acetogenesis does dominate. And there could be interesting issues about genetics and that as well. For example, wood eating termites, not detritus eating termites  but wood eating termites a reductive acetogenesis tends to dominate in their hindgut. It dominates in the hunger of ostriches as well. It also actually dominates in about two thirds of humans. Only about 1/3 of humans are methanogenic. So what switches it on what switches off? Can we work that out? Can we look for those particular triggers, particular switches?

AS

You mentioned a number of species, termites, humans or ostriches. Are there any patterns across nature that sort of say that this type of animal, this type of ecosystem favours certain type of either acetogenesis or methanogenesis.  

AK

It would be lovely if there was and I reviewed a lot of this literature quite a while ago now and look through it in a great deal of detail. And realistically, we were not able to come up with any definitive factors of size, invertebrate or vertebrate ,  warm blooded or cold blooded, even whether the carnivorous or herbivorous there suggested that I mean, one of the big issues that always comes as a rite of passage might have an effect, but it might but in low these animals you've looked at it's really not a big issue. The temperature isn't an issue either. It's interesting that for example, some of the very large snakes and crocodiles which totally carnivorous actually produced methane a lot of other plant eating insects, kangaroos, ostriches, etc which basically herbivorous don’t produce methane. And yet, then we've got a lot on the other side of that as well that do produce methane that are totally herbivorous so.

AS

You mentioned humans were roughly two thirds acetogenic and one third methanogenic. Are there other species where there's a divide like that, that we're aware of?

AK

Not that I don't think that they are that we are aware of, which is sort of interesting in itself. Now I think I couldn't put the hell of literature. But I think I have seen that there could be genetic reasonings between this in humans as well. And basically, switching diets for example won't change, whether they're methanogenic or reductively acetogenic, which is quite interesting in itself.

AS

I guess there's two things that come from that. The first is his age and the time that this is set, and whether it's something that's set very early in life or in utero, and that has an effect. And the second thing is if there's not really any clear patterns within nature, some animals are acetogenic. Some are methanogenic and then there are a species like us, that can be either or is it I guess naive to say that it's not fixed in nature so it can be changed and the different species are a map that nature has provided? And our challenge is just to work out how to read that map.

AK

that would be one way of looking at it, and that would be a different possibility. I mean, it's really difficult to say why some species of animals with methanogenic and some are reductively actetogenic. Also, whether it can be changed is an interesting issue. And when it can be changed on that, on that area. There we were. We had done some research, as well to look at whether we would be able to from a general perspective anyway, if we're going to look at trying to manipulate the rumen ecosystem by introducing microbes that we know that if we have a an empty or blank niche in there that we can put something in such as Synergistes jonesii when we introduce animals Leucaena or if they change diets, and we can address something that would already come into their ecosystem.

Unknown 5:49

We can always Can you hear that? They said yep, power out the back if you don't mind just waiting for 30 seconds. A minute while he gets away.

Unknown 6:04

Yeah.

Unknown 6:13

I loved it loves to be part of the world.

Unknown 6:17

So sorry, where were we again?

Unknown 6:20

Just can you is it still really loud or is it not too bad?

Unknown 6:23

I can't hear it now. Okay.

Unknown 6:26

You were explaining the introduction of the integrating Lukina to detoxify any negative.

AK

Yeah. Well, that's just an example that if there's nothing else in the niche, then you can put something into that complex ecosystem. But introducing organisms into a complex ecosystem and trying to get them to compete with organisms that are already undertaking a role there. And you want to try to move them out and move these ones in, could be considerably more difficult and trying to work out. Okay. No matter what you're trying to manipulate the rumen. When is the best time to try to get a permanent change, made? It's pretty obvious. You know, when animals are born, they're basically their gut is sterile or effectively sterile, and then it develops and builds quite quickly. And it's just when you know which organisms get in there. Some intermediate so that you know, taking it from one particular level of nutrition to another level of nutrition. So when can we actually introduce that particular microbes in there and get them to stay there for the for the whole thing? That it's a big question, and it's an important question, if we’re ever going to try to successfully manipulate the rumen by for example, I'll go back to fibre degradation. Again. For example, if we want to introduce a more highly fibrolytic microbe into that. We do we need to get that in before anything else is in there. Can we knock something else out by getting it in later on? Yeah, that that's quite a quite an issue.

AS

You've also got the fact that different species you mentioned you've got certain reptiles will be born from eggs and they'll never see their parents or have any interaction with their parents, certain birds are also born from eggs, but there will be some interaction with the parents and then you've got mammals who alive or that have different interactions. So how much of that maternal microbiome gets transferred across is also something that's it's very, very variable.

AK

Yeah, yeah, and how much has that got to do with the animals themselves and their selective, their genetics or their selective pressure in the gut to select for a certain population of microbes as well. And you know, what, what are these animals? What do these young animals have available to them in terms of microbiology, you know, they have to, they have to, they can only be colonized by the microbes that they're going to be exposed to. So if we can limit that to an extent and get the preferred microbes in that we want. Be they reductive acetogens and not You know, be they higher quality cellulolytic microbes, fibrolytic microbes. Yeah, I think that's that's that's the question is, is what's our timing and keeping will eventually when they're exposed to say some of the more original microbiome from the parents pool will that recolonise or not?

AS

So we where do you see the next steps in terms of understanding how I guess the next step, not just in understanding but in in making a tangible step in terms of the rumen microbiome fermentation towards something that's more acetogenic and less methanogenic? 

AK

Yeah, well, I guess I guess it does come down to that understanding. And there's two directions where we could go with that is one is the trying to introduce the microbes, trying to introduce from other ecosystems where we know that they are dominant and get them out of those ecosystems. And get them into the into the animals at an appropriate time in the life of those animals and see if that can work. But the other thing is actually understanding whether just simply changing some of it or trying to change some of the conditions that are occurring within the rumen itself. Might might might enhance that. So more so it's a really a probiotic I guess and a prebiotic type of approach where you're going to be not just having the correct microbes present, but also having the correct conditions that going to allow them to to proliferate and, and maintain those populations for a long period of time.

AS

Given the you've got acetogenesis and methanogenesis in all species, are there any opportunities to use laboratory animals that are much cheaper and smaller and shorter generation periods such as mice or other if there's any foregu t for meeting small mammals to to understand what may or may not work in the triggers and then scale it up?

Unknown 12:28

I think that would be difficult. I mean, it might be useful to be able to understand some basic parameters or some some basic rules, if you like, of the why things happened, but the the specifics of it so it might help in a general way but in the specifics of it, there's enough differences between animal species and that and what they do. And as I was saying, whether they're going to be, you know, or any, if we look at the natural environment and look at the huge amount of differences between what's productive is energetic and what's pathetic, genic and how it varies. Throughout all sorts of different types of life. That being able to then transfer that knowledge across from a very different species could prove quite difficult,

 because one interesting issue on that is we already know that sheep or for many, many years, way back last century, sheep were used as a model for cattle. We now know that right from a microbiome point of view, sheep are quite different to cattle, even when they've got the same species of microbes present. They change their rumen is quite dynamic in in how rapidly it changes in terms of microbial communities. Whereas in cattle and also interestingly, in kangaroos it's quite stable while they're on the same diet

AS

do we know where goats fit into that and goats similar to sheep of are they to cattle and all those other former others or Deer or other other small ruminant? Yeah.

AK

I mean, there's there's not too many longitudinal studies ever been done on those there might be now from throughout Asia and some of those places through there and I haven't looked at the literature, but I don't think there is. So we've got a lot of points in time. If you like, data for those types of animals. But what we don't do is have studies showing how their microbiome changes over time. On the same feedstuffs on different feed cells.

AS

Excellent, thank you. Is there any good thank you very much. Thank you very much. Is there anything else that we haven't covered that you think is worthwhile mentioning?

AK

Well, I mean, I guess the other thing is, is the use of feeds and feedstuffs to manipulate the microbiome as well, because there's an interaction as well and when we come to, I mean, obviously the seaweed things comes into it.

And the pros and cons of that, but also the use of lipid based feed additives for example, and there could be quite a lot of other things in various fields

that we really don't know at this stage, what impact that's going to go what impact that does have on on the gut microbiology including on methanogenesis, and acetogenisis Is that 

Yeah, I think the thing also is that if we're gonna get the value in terms of nutrition and feeding animals from reducing methane, we actually have to channel those products into something else that the animal can use that has an energy value chain, the whole idea of just blocking methanogenesis won't really give you any benefit in terms of production.

AS

So that then becomes critical in terms of what's the value for the producer if they put an extra cost on yesterday's environmental climate impact or benefit, but there's no direct benefit for them. Plus, you've got the fact that there's I guess, if it's a 10 to 14% energy cost, it'd be like having a leaky tap.

AK

Yeah, well, you know, I remember saying to say to producers, you know, about you know, why why you should be looking at channelling methane into something else and yeah, you grow that pasture out there you grow those crops out there to feed the animals. First. If I just went out and said, Okay, take take a tenth of that out and just burn it, throw it away. You wouldn't be real happy about that. But that's exactly what you're doing at the moment. Yeah, basically, it's, it's just going and so if you want to get the value out of that extra extra material that you're growing, to feed those animals. You want to make sure that it's not going up into the atmosphere.

AS

We do have one very common practice with cattle and sheep with ruminants of actually adding a lot of microbes to fermented feeding things like silage, fluid microbes. So this adding different different live cultures into that rumen environment. Is there any learnings from how that affects or silage feeding affects the rumen microbiome that could be used to help our understanding? Yeah,

AK

I don't know. I'm not sure I'm not sure how, how long those particular microbes last in the in the rumen ecosystem and whether they just simply are effectively another source of protein to the animal, because they're typically not microbes that were metabolize in the rumen environment at all.

AS

Is that because of the pH of the salvage?

AK

No, it's, it's just that those those particular microbes are not all that highly strictly anaerobic, I mean, the antibiotics, but they've been they've been selected to survive in fairly highly aerobic conditions to under the under the high competition, and the high density of microbes and a really heavily strict anaerobic conditions. They don't seem to do much. They just stay washed through pretty long. Okay. Yeah, not saying they killed in the rumen. But they do wash through. Yeah, provide a bit of extra bit of extra protein but even then, I mean, it's trying to think about what numbers they would be talking about bacteria being at about 10 to the 11 per mil, in rumen content, so and that's what's flowing out. So if you're adding in an extra 10 to the 10 to the 710 the eight you're not really adding much to it.

AS

Well, thank you very, very much, Athol. It's been an absolute pleasure speaking to