(Re)introducing the microbial buddy system

By Laurence Clarke

Co-extinction may be the most common form of extinction there is. From the Tasmanian tiger to the gastric-brooding frog, it’s no secret that lots of Australia’s animals have gone extinct. But many tiny microorganisms were dependent on these large animals. What happened to these microbes after the loss of their bigger buddies, and, if we can bring the animals back, will their microbes return too?


A burrowing bettong returns to South Australia. Credit: Arid Recovery

One of the few places where this question can be answered is the Arid Recovery reserve. This not-for-profit reserve was established near Roxby Downs in northern South Australia as a conservation initiative. Since the late 1990s, Arid Recovery has been trying to restore the ecosystem by removing introduced animals (livestock, rabbits, feral cats) and replacing them with the three native B’s (burrowing bettongs, greater bilbies, western barred bandicoots) and a rat (well, the greater stick-nest rat). These species were all locally extinct prior to their reintroduction at the Arid Recovery reserve. But, what did this do to the microbes?

Microbes like fungi perform important ecosystem functions, such as breaking down decaying matter and helping plants take up nutrients. We used high-throughput DNA sequencing to compare the fungi in the soil inside and outside the Arid Recovery reserve. Sure enough, soil from sites inside the reserve, with the reintroduced natives, had different fungal communities to sites outside, dominated by exotic species (rabbits, cows etc.). Some fungi were only found inside the reserve, and some of these were coprophilous (literally “poo-loving”) fungi. If the fungi are living in the poo of the native mammals, that provides a direct link between the reintroduced species and the soil fungi.

School students assisted us by collecting poo inside the reserve (big thanks to Port Lincoln High School Indigenous Ranger Cadetship programme!) and I sequenced the fungi in the poo (or scats). There were about 190 different fungi in the scats, and most of the scat fungi were also found in the soil samples (about 83%). Surprisingly, more than 20 of these fungi were only found in soil from inside the reserve.

So it looks like reintroducing native mammal species to the reserve brought in new fungal species as well!

So what does this mean?

  • Number 1, when we introduce exotic species to a new environment, be it cats or cattle, chances are they’ll bring new microbes along with them too.
  • Number 2, reintroducing native species can help restore ecosystems by changing the microbes in the soil.
  • Number 3, if we lose species from an environment, we’re probably losing a lot more than just what we can see with the naked eye. Even if we can reintroduce native species, if the microbes that depended on them have gone extinct, restoring the full suite of ecological interactions may be impossible.

This last point is the most sobering. Once ecosystem interactions are lost, we may only be able to replace them superficially. However, our work shows that reintroducing large native mammals can also help restore the microbial ecology.

For a comprehensive look at this project, see the full article in Molecular Ecology:

Clarke LJ, Weyrich LS, Cooper A (2015) Reintroduction of locally extinct vertebrates impacts arid soil fungal communities. Molecular Ecology, 24: 3194-3205. doi: 10.1111/mec.13229

STOP PRESS: A French group has just published a similar study in Biology Letters on how introduced rabbits have changed the soil fungi on subantarctic islands. It looks like the fungal communities aren’t recovering even a long time after the rabbits are removed. Check out the Science News post for a summary.


2 thoughts on “(Re)introducing the microbial buddy system

  1. Charlotte

    Hi Laurence, very exciting research! Just quickly, (haven’t read the published article yet so the answer might be in there) how do you know the microbes you found inside the fence weren’t merely brought with the bettongs from WA, which presumably has a different microbial biome?

    1. Australian Centre for Ancient DNA Post author

      Great question Charlotte, and one we can’t answer yet! There’s a good chance the fungi are from the microbiomes of the reintroduced mammals, especially the bettongs seeing as they’re the most abundant at Arid Recovery. It would be really interesting to compare the fungi in the scats (and soil) from the WA bettong populations with what we got from the Arid Recovery reserve to see how they match up. The other possibility is that the fungi were already present at low levels in the soil at Arid Recovery, and, through the reintroduced species acting as ‘ecosystem engineers’, some of those have increased to detectable levels.


Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s