Artificial selection improves pollutant degradation by bacterial communities
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (Arcadia Science)
Abstract
Artificial selection is a promising way to improve microbial community functions, but previous experiments have only shown moderate success. Here, we experimentally evaluate a new method that was inspired by genetic algorithms to artificially select small bacterial communities of known species composition based on their degradation of an industrial pollutant. Starting from 29 randomly generated four-species communities, we repeatedly grew communities for four days, selected the 10 best-degrading communities, and rearranged them into 29 new communities composed of four species of equal ratios whose species compositions resembled those of the most successful communities from the previous round. The best community after 18 such rounds of selection degraded the pollutant better than the best community in the first round. It featured member species that degrade well, species that degrade badly alone but improve community degradation, and free-rider species that did not contribute to community degradation. Most species in the evolved communities did not differ significantly from their ancestors in their phenotype, suggesting that genetic evolution plays a small role at this time scale. These experiments show that artificial selection on microbial communities can work in principle, and inform on how to improve future experiments.
Article activity feed
-
Good question. We'll have to look into it. From Fig. 3, you can see that they're actually quite similar. As we pointed out, their phenotypes barely changed over the experiment. But we'll check and clarify it in the text.
-
The CFUs/ml done on day 0 show that they are quite different across species. We decided not to correct for these differences for simplicity. We also did not analyse in detail whether this has any consequences (e.g. low population size making extinctions more likely). But all the data are available in the attached Excel sheets.
-
Thanks a lot Manon! Also for reviewing it, I really appreciate your thoughts!
-
When isolating species to use for the next round, we tried to collect as many colonies as grew on the plate to try to maximize within-species diversity. But you're right that this still probably introduced a very strong bottleneck. We will add a comment on this.
-
We have just whole-genome sequenced them. What do you think would be interesting to look for?
-
Same, in the pdf they are consistent.
-
Seems to be an error from the conversion from pdf to html in biorxiv. The pdf is fine..
-
Seems to be an error from the conversion from pdf to html in biorxiv. The pdf is fine...
-
We listed the species in Table S1. It's true that they are often the same onees (mostly 4 species). All species are always inoculated at the same OD, so it shouldn't be a problem of initial concentration. Perhaps we will add a sentence to the main text clarifying this. Thank you!
-
It's what we managed until COVID lockdown. I suppose it should say that somewhere in the methods section.
-
We therefore conclude that evolution at this timescale has not had profound effects on the species’ phenotypes.
As a general thought, I wonder if, while you don't see a profound effect of evolution on the species phenotype yet and potentially no specific mutant with enough fitness gain to have taken over a species population, the within-species genetic heterogeneity that's likely to be present for each species can influence the global set of interactions and the overall degradation phenotype/ability.
-
Even though the challenges of ensuring ecological and evolutionary stability remain open, we argue that this first proof-of-concept supports the blind approach to automate the breeding of bacterial communities with optimal functions.
Thank you for this very interesting study. This represents a considerable amount of experimental work, and the strategy behind the directed evolution is clear and clever.
-
monoand
Typo
-
monoand cocultures
Typo: this should be mono- and co-cultures
-
disas-sembly
Typo?
-
The best individual degraders were Pf, Ct and At1 (mean degradation: 66%, 58% and 50% respectively), while Af, Ea and At2 were the worst (mean degradation: 2%, 2% and 4% respectively, Fig. 3B, D).
It is unclear here whether the authors are measuring the degradation activity of the species isolated from the best degrading communities after the 18 rounds or the original species.
-
At1+Ct+Af+Ac
Have these species (and any other species) in this work been sequenced?
-
Overrepresented
Just a tiny detail, but there are inconsistencies in whether the authors use overrepresented, over-represented, underrepresented or under-represented
-
overor
Typo?
-
5
Typo?
-
18 times
Is there a reason behind this choice? Did you want to keep experimenting until you reach a certain degradation score?
-
extinctions
Are the species going extinct always the same? If this is the case, I wonder if this could highlight some potential specific physiological features or simply that this species may have been consistently inoculated at a lower concentration. Overall, I think it could be very interesting/informative to mention this information.
-
Weselected
Typo: space missing
-
four species of similar relative abundances.
While the species have been normalized to the same OD before inoculation, do the authors know if this roughly represents similar cell concentration across species? Are all inoculations close to a 1:1:1:1 ratio?
-
-