Multistep diversification in spatiotemporal bacterial-phage coevolution

被引:19
作者
Shaer Tamar, Einat [1 ]
Kishony, Roy [1 ,2 ,3 ]
机构
[1] Technion Israel Inst Technol, Fac Biol, Haifa, Israel
[2] Technion Israel Inst Technol, Fac Comp Sci, Haifa, Israel
[3] Technion Israel Inst Technol, Fac Biomed Engn, Haifa, Israel
基金
以色列科学基金会;
关键词
ESCHERICHIA-COLI; ANTAGONISTIC COEVOLUTION; EVOLUTIONARY DYNAMICS; VIBRIO-CHOLERAE; ARMS-RACE; HOST; PATHOGEN; PROCHLOROCOCCUS; BACTERIOPHAGES; POPULATION;
D O I
10.1038/s41467-022-35351-w
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The evolutionary arms race between phages and bacteria, where bacteria evolve resistance to phages and phages retaliate with resistance-countering mutations, is a major driving force of molecular innovation and genetic diversification. Yet attempting to reproduce such ongoing retaliation dynamics in the lab has been challenging; laboratory coevolution experiments of phage and bacteria are typically performed in well-mixed environments and often lead to rapid stagnation with little genetic variability. Here, co-culturing motile E. coli with the lytic bacteriophage T7 on swimming plates, we observe complex spatiotemporal dynamics with multiple genetically diversifying adaptive cycles. Systematically quantifying over 10,000 resistance-infectivity phenotypes between evolved bacteria and phage isolates, we observe diversification into multiple coexisting ecotypes showing a complex interaction network with both host-range expansion and host-switch tradeoffs. Whole-genome sequencing of these evolved phage and bacterial isolates revealed a rich set of adaptive mutations in multiple genetic pathways including in genes not previously linked with phage-bacteria interactions. Synthetically reconstructing these new mutations, we discover phage-general and phage-specific resistance phenotypes as well as a strong synergy with the more classically known phage-resistance mutations. These results highlight the importance of spatial structure and migration for driving phage-bacteria coevolution, providing a concrete system for revealing new molecular mechanisms across diverse phage-bacterial systems.
引用
收藏
页数:12
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