The evolution of reduced facilitation in a four-species bacterial community
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Abstract
Microbial evolution is typically studied in mono-cultures or in communities of competing species. But microbes do not always compete and how positive inter-species interactions drive evolution is less clear: Initially facilitative communities may either evolve increased mutualism, increased reliance on certain species according to the Black Queen Hypothesis (BQH), or weaker interactions and resource specialization. To distinguish between these outcomes, we evolved four species for 44 weeks either alone or together in a toxic pollutant. These species initially facilitated each other, promoting each other’s survival and pollutant degradation. After evolution, two species ( Microbacterium liquefaciens and Ochrobactrum anthropi ) that initially relied fully on others to survive continued to do so, with no evidence for increased mutualism. Instead, Agrobacterium tumefaciens and Comamonas testosteroni ( Ct ) whose ancestors interacted positively, evolved in community to interact more neutrally and grew less well than when they had evolved alone, suggesting that the community limited their adaptation. We detected several gene loss events in Ct when evolving with others, but these events did not increase its reliance on other species, contrary to expectations under the BQH. We hypothesize instead that these gene loss events are a consequence of resource specialization. Finally, co-evolved communities degraded the pollutant worse than their ancestors. Together, our results support the evolution of weakened interactions and resource specialization, similar to what has been observed in competitive communities.
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he reads were aligned against all merged ancestral reference genomes with no secondary mapping in order to avoid cross-mapping
I am wondering how genetically different are all the species. How much of the genomes of the species overlap? How much of each species' genome was recovered without cross-mapping?
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1 3-species co-culture, 1 4-species co-culture
Are the co-cultures inoculated with a 1:1 ratio for each species?
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Thank you for this very interesting work. I agree that studying the roles of interactions in microbes' evolution and our ability to predict microbial community evolution is crucial. This works is a very nice contribution to this challenging goal.
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as we detected some within-species phenotypic diversity in growth and degradation (Fig. S1, Fig. S2
FigS1 and FigS2 indeed show the diversity in growth. Is the diversity in degradation an expected phenotype as a consequence of the growth differences? Or is this statement about diversity in degradation associated with a measured trait?
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The only mutation present uniquely and repeatedly in CCt was in the acuC gene, which is expected to affect gene expression
With the sequencing data from the different transfers, is it possible to trace back when the acuC appeared?
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But many variants did not fix and remained at intermediate frequencies
The authors mentioned before that the experiment represents around 300 generations per species. Do they expect to see the fixation of many variations that provide a fitness advantage in 300 generations? Have the authors an idea of what the trajectories would be if they pursued the experiment for another 200 generations, would they see fewer variants with intermediate frequency? 300 generations are already a lot and it took almost a year, so I am just wondering if now that they see these trajectories, they could predict the trajectory for more generations.
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Ct accumulated a higher number of variants compared to when it was evolving alone
Have you characterized the variant population earlier than transfer 11? While Ct accumulated more variations when evolving in the community, how wonder how this compares to the initial population, and how this could inform us about the evolution rate. Also, it could be interesting to see if all the species had a similar diverse population at the beginning and whether it may have influenced the outcome of the experiment.
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Table x
This might be a typo. Is the number of the Table missing?
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