Exploring microbial community assembly on single carbon sources

Goldford et al. 2018. Emergent simplicity in microbial community assembly. Science.

This is a summary of our DalMUG journal club discussion of this paper written by Gavin Douglas

Summary

The take-home messages of this paper are that community assembly is reproducible at high taxonomic levels (on simple media) and there is widespread cross-feeding between genera that explains the community assembly. Certain microbial ecologists present at our discussion felt that these take-home messages were unsurprising and that they echoed many previous findings, especially in the aquatic microbial ecology literature. Nonetheless, the scientific logic of this paper was very clear and this paper represents great exposure for microbial ecology.

Points of Interest

  • Clear demonstration of reproducible families assembling on simple C sources (and that this isn’t the case at finer resolutions)
  • Interesting to see tSNE with PICRUSt predictions. Would be nice to know how typical microbial ecology ordination methods separated the C sources
  • Secretion and not cell lysis seems to be the main way that by-products are transferred, based on phase-contrast microscopy
  • Very clear experiments demonstrating capability for cross-feeding between all 4 isolated pairwise microbes
  • The extension to MacArthur’s consumer-resource model (that allows by-products to re-enter the resource pool) was a convincing way of arguing that taxonomic stability can arise based on the stable cross-feeding of microbes.

Points of Confusion

  • Would have been interesting to look at original community to see if they could grow on the byproducts
  • Interesting use of ternary plots, but their explanation of how to read it differs from examples online, such as here: https://brocku.ca/earthsciences/people/gfinn/petrology/ternary5.gif
  • Also not sure why Pseudomonadaceae in their example is 0.36 based on the dotted-line… Looks like 0.25 to us
  • Not surprising to see the reproducibility of family-level relative abundances in their first experiments. It’s well-known that you will get similar microbes using a selective media
  • Since Pseudomonas is a famous generalist it’s also not surprising it can survive off of the by-products so well
Written on September 12, 2018