Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies

Abstract

Colony growth is a common phenomenon of structured populations dispersed in nature; nevertheless, studies on the spatial distribution of colonies are largely insufficient. Here, we performed a systematic survey to address the questions of whether and how the spatial distribution of colonies was influenced by the genome and environment. Six Escherichia coli strains carrying either the wild-type or reduced genomes and eight media of varied nutritional richness were used to evaluate the genomic and environmental impacts, respectively. The genome size and nutritional variation contributed to the mean size and total area but not the variation and shape of size distribution of the colonies formed within the identical space and of equivalent spatial density. The spatial analysis by means of the Voronoi diagram found that the Voronoi correlation remained nearly constant in common, in comparison to the Voronoi response decreasing in correlation to genome reduction and nutritional enrichment. Growth analysis at the single colony level revealed positive correlations of the relative growth rate to both the maximal colony size and the Voronoi area, regardless of the genomic and nutritional variety. This result indicated fast growth for the large space assigned and supported homeostasis in the Voronoi correlation. Taken together, the spatial distribution of colonies might benefit efficient clonal growth. Although the mechanisms remain unclear, the findings provide quantitative insights into the genomic and environmental contributions to the growth and distribution of spatially or geographically isolated populations.

Experimental evolution for the recovery of growth loss due to genome reduction

“…Intriguingly, a positive correlation was observed between the growth fitness and the carrying capacity of the Evos ( Figure 1D ). It was consistent with the positive correlations between the colony growth rate and the colony size of a genome-reduced strain ( Hitomi et al, 2022 ) and between the growth rates and the saturated population size of an assortment of genome-reduced strains ( Kurokawa et al, 2016 ). Nevertheless, the negative correlation between growth rate and carrying capacity, known as the r/K selection ( Engen and Saether, 2017 ; Luckinbill, 1978 ), was often observed as the trade-off relationship between r and K in the evolution and ecology studies ( Marshall et al, 2023 ; Molenaar et al, 2009 ; Wortel et al, 2018 ).…”

“…These efforts have been made to discover the minimal genetic requirement for a free-living organism growing under the defined conditions ( Aida and Ying, 2023 ; Breuer et al, 2019 ; Hutchison et al, 2016 ). It resulted in the finding of the coordination of genome with cell growth, that is, genome reduction significantly decreased the growth rate of Escherichia coli cells independent of culture media or growth forms ( Hitomi et al, 2022 ; Xue et al, 2021 ; Kurokawa et al, 2016 ). Slow growth or fitness decline was commonly observed in the genetically reduced ( Kurokawa et al, 2016 ; Karcagi et al, 2016 ) and chemically synthesized genomes ( Hutchison et al, 2016 ; Gibson et al, 2010 ).…”

Experimental evolution for the recovery of growth loss due to genome reduction

“…1D). It was somehow consistent with the positive correlations between the colony growth rate and the colony size of a genome-reduced strain 11 and between the growth rates and the saturated population size of an assortment of genome reduced strains 13 . Nevertheless, the negative correlation between growth rate and carrying capacity, known as the r/K selection 30,31 was often observed as the trade-off relationship between r and K in the evolution and ecology studies 32 33,34 .…”

“…It seemed that the present experimental evolution did not obey the r/K selection theory 30, 31 , which was known as the trade-off relationship (negative correlation) between the growth rate and the carrying capacity 32,33 . Taking account of our previous finding that the colony growth rates of genome-reduced strains were proportional to the colony sizes 11 , the collapse of the trade-off law likely resulted from genome reduction. As the trade-off between growth fitness and carrying capacity was proposed to balance the cellular metabolism that resulted from the cost of enzymes involved 33 , the deleted genomic sequences might play a role in maintaining the metabolism balance.…”

“…These efforts have been made to discover the minimal genetic requirement for a free-living organism growing under the defined conditions [8][9][10] . It resulted in the finding of the coordination of genome with cell growth, i.e., genome reduction significantly decreased the growth rate of Escherichia coli (E. coli) cells independent of culture media or growth forms [11][12][13] . Slow growth or fitness decline was commonly observed in the genetically reduced 13,14 and chemically synthesized genomes 10,15 .…”