Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization

Nordgaard, Mathilde; Blake, Christopher; Maróti, Gergely; Hu, Guohai; Wang, Yue; Strube, Mikael Lenz; Kovács, Ákos T.

doi:10.1016/j.isci.2022.104406

Cited by 26 publications

(42 citation statements)

References 87 publications

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“…Ancestor bacterial strains and evolved population samples used in this study are from previous studies [41][42][43][44] . Frozen samples from each adaptation model were revived via cultivation in Lysogeny broth (LB; Lennox, Carl Roth; 10 g•L -1 tryptone, 5 g•L -1 yeast extract, and 5 g•L -1 NaCl) medium for 16 hours at 30℃ and 37℃ for B. thuringiensis and B. subtilis, respectively, before harvesting the cells for genomic DNA extraction.…”

Section: Methodsmentioning

confidence: 99%

“…2). To test whether population size contribute to this parallelism difference 67 , we estimate the approximate population size (here we calculate the biofilm production for comparison) of each condition from the previous data [41][42][43][44] , range 8.40E+05 to 3.29E+07, 1.13E+03 to 1.05E+06, 3.33E+08 to 1.99E+10, and 6.00E+04 to 4.68E+06…”

Section: Parallelism and Genetic Targets Of Selectionmentioning

confidence: 99%

“…Re-sequencing of single evolved isolates from independent populations and different time points revealed mutations in genes related to different bacterial traits. The examined evolved isolates also displayed robust biofilm formation in response to plant polysaccharides, impaired motility, and altered growth on plant-derived compounds 44 .…”

Section: Introductionmentioning

confidence: 96%

“…In these laboratory evolution setups, 5 to 7 parallel lineages (i.e., subsequent populations with an individual evolutionary trajectory) were followed using 30 to 40 transfers. The detailed descriptions of each experiment were previously published [41][42][43][44] .…”

Section: Introductionmentioning

confidence: 99%

“…For B. thuringiensis , experimental evolution was performed using two approaches, a plastic bead attached biofilm model (Bth_bead) 41 and Arabidopsis thaliana root colonization model (Bth_root) 42 . Similarly, B. subtilis , a static air-medium floating biofilm transfer mode (Bs_pellicle) 43 and an A. thaliana root colonization model (Bs_root) 44 were used. Thus, for each bacterial species, biofilm formation proceeded under abiotic conditions (plastic bead or air-liquid interface) and on biotic surfaces ( A. thaliana root).…”

Section: Introductionmentioning

confidence: 99%

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Species and condition shape the mutational spectrum in experimentally evolved biofilms

Wang

Liu

et al. 2022

Preprint

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Laboratory experimental evolution provides a powerful tool for studying microbial adaptation to different environments. To understand the differences and similarities of the dynamic evolutionary landscapes of two model species from the Bacillus genus as they adapt to abiotic and biotic surfaces, we revived the archived population samples from our four previous experimental evolution studies and performed longitudinal whole-population genome sequencing. Surprisingly, higher number of mutations, higher genotypic diversity, and higher evolvability were detected in the biotic conditions with smaller population size. Different adaptation strategies were observed in different environments within each species, with more diversified mutational spectrum detected in biotic conditions. The insertion sequences of Bacillus thuringiensis are critical for its adaptation to the plastic bead-attached biofilm environment, but insertion sequence mobility was a general phenomenon in this species independent of the selection condition. Additionally, certain parallel evolution has been observed across species and environments, particularly when two species adapt to the same environment at the same time. Further, the higher degree of genetic diversification observed in biotic selective environments indicates an increased spatial niche heterogeneity and a nutritional source difference created by the plant host that provided a strong strength of selection during the adaptation process. Together, these results provide the first comprehensive mutational landscape of two bacterial species biofilms that is adapted to an abiotic and biotic surface.

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Section: Methodsmentioning

confidence: 99%

Section: Parallelism and Genetic Targets Of Selectionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Species and condition shape the mutational spectrum in experimentally evolved biofilms

Wang

Liu

et al. 2022

Preprint

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Exploring Bacillus subtilis: Ecology, biotechnological applications, and future prospects

Akinsemolu,

Onyeaka,

Odion

et al. 2024

J Basic Microbiol

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From its early identification by Christian Gottfried Ehrenberg to its current prominence in scientific research, Bacillus subtilis (B. subtilis) has emerged as a foundational model organism in microbiology. This comprehensive review delves deep into its genetic, physiological, and biochemical intricacies, revealing a sophisticated cellular blueprint. With the incorporation of advanced techniques such as clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein 9 and integrative computational methodologies, the potential applications of B. subtilis span diverse sectors. These encompass its significant contributions to biotechnology, agriculture, and medical fields and its potential for aiding environmental cleanup efforts. Yet, as we move forward, we must grapple with concerns related to safety, ethics, and the practical implementation of our lab findings in everyday scenarios. As our understanding of B. subtilis deepens, it is evident that its contributions will be central to pioneering sustainable solutions for global challenges in the years to come.

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Microbes to support plant health: understanding bioinoculant success in complex conditions

Poppeliers

Sanchez-Gil

Jonge

2023

Current Opinion in Microbiology

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Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization

Cited by 26 publications

References 87 publications

Species and condition shape the mutational spectrum in experimentally evolved biofilms

Species and condition shape the mutational spectrum in experimentally evolved biofilms

Exploring Bacillus subtilis: Ecology, biotechnological applications, and future prospects

Microbes to support plant health: understanding bioinoculant success in complex conditions

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