Engineering complex communities by directed evolution.
Journal
Nature ecology & evolution
ISSN: 2397-334X
Titre abrégé: Nat Ecol Evol
Pays: England
ID NLM: 101698577
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
received:
06
08
2020
accepted:
28
03
2021
pubmed:
15
5
2021
medline:
3
8
2021
entrez:
14
5
2021
Statut:
ppublish
Résumé
Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modelling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search of dynamically stable and ecologically resilient communities with desired quantitative attributes.
Identifiants
pubmed: 33986540
doi: 10.1038/s41559-021-01457-5
pii: 10.1038/s41559-021-01457-5
pmc: PMC8263491
mid: NIHMS1688330
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1011-1023Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM133467
Pays : United States
Commentaires et corrections
Type : CommentIn
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