Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method

Frey, Pascal M.; Bär, Julian; Bergadà-Pijuan, Judith; Lawless, Conor; Bühler, Philipp; Kouyos, Roger D.; Lemon, Katherine P.; Brugger, Silvio D.

doi:10.1128/msystems.01323-20

Cited by 28 publications

(5 citation statements)

References 18 publications

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“…Exogenous DNA reduces infection by fungal and bacterial pathogens in a self-/non-selfnonspecific way. To determine the effects of DNA treatment on the quality of the plant as a host for microbial pathogens, we aimed to take the perspective of the microbes and therefore, we decided to quantify population densities reached at a specific time point after challenge as an approximation of microbial reproductive fitness [32][33][34] . Among four fungal strains tested, we detected no significant effect of DNA treatment on the density reached by Colletotrichum lindemuthianum or Fusarium oxysporum (GLM, P > 0.05, n = 10, Fig.…”

Section: Resultsmentioning

confidence: 99%

The CpG-dependent plant immune response to self-DNA triggers defence hormone signalling and improves fitness

Durán-Flores

Heil

2023

Preprint

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The accumulation of DNA in the cytoplasm or extracellular space is a signal of danger. Plants respond to this signal with a self/non-self-specific activation of early immune signalling events. Here, we asked whether this specificity translates to fitness-relevant resistance to natural enemies. We treated common bean (Phaseolus vulgaris) plants with self-DNA and with non-self-DNA from other plant species. Self-DNA treatment induced jasmonic acid and decreased feeding by a chewing herbivore (Spodoptera frugiperda), while self- and non-self-DNA induced salicylic acid and reduced the population densities of two fungal pathogens (Botrytis cinerea and Sclerotinia sclerotiorum) and of four bacterial pathogens (Enterobacter sp. strain FCB1, Pseudomonas syringae pv. phaseoli and pv. syringae, and Xanthomonas axonopodis pv. phaseoli). Strikingly, a single self-DNA-treatment increased seed production under field conditions in two seasons ca. 1.5-fold and 3.2-fold, while non-self-DNA had lower or no detectable effects. Stronger responses to self- than non-self-DNA seemingly contradict immunological theory. In mammalian immune cells, toll-like receptor 9 (TLR9) is activated by microbial DNA but also by mitochondrial (mt)DNA that is rich in unmethylated CpG motifs. Using bean suspension cells, we observed stronger immunogenic effects of genomic DNA than chloroplast DNA or mtDNA. Moreover, in vitro methylation or cleavage of CpG motifs reduced – without eliminating – the H2O2-inducing properties of DNA. We conclude that the plant immune response to DNA comprises a self/non-self-specific induction of major defence hormones that can be adaptive under natural enemy pressure and that unmethylated CpG motifs contribute to the immunogenic effects of DNA in plants.

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Section: Resultsmentioning

confidence: 99%

The CpG-dependent plant immune response to self-DNA triggers defence hormone signalling and improves fitness

Durán-Flores

Heil

2023

Preprint

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“…To compare the reproductive fitness of the clinical isolates, bacterial quantitative fitness analysis (BaQFA) was carried out as previously described ( 58 ). In brief, S. aureus strains freshly grown on TSB agar plates were harvested, resuspended in PBS to an OD 600 of 0.1, and subsequently diluted 1:40 in PBS.…”

Section: Methodsmentioning

confidence: 99%

Limited Adaptation of Staphylococcus aureus during Transition from Colonization to Invasive Infection

et al. 2023

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“…In this approach, growth parameters, such as the maximum growth rate (V max ), carrying capacity (K), and area under the curve (AUC), are calculated from absorbance values and used as proxies for fitness (Kugelberg et al 2005;Hansen et al 2007;Hegreness et al 2008;Paulander et al 2009;McDonald et al 2012; Handling Editor: Kerry Geiler-Samerotte. Ketola and Saarinen 2015;Kang et al 2019;Santiago et al 2020;Frey et al 2021). Populations with increased V max , K, or AUC values are considered to be more fit relative to those with lower values.…”

Section: Introductionmentioning

confidence: 99%

“…The first method uses data obtained from growth curves as an indirect measure of fitness and is one of the most commonly used methods outside of the experimental evolution field (Warringer et al 2003 ; Kugelberg et al 2005 ; Paulander et al 2009 ; Łapińska et al 2022 ). In this approach, growth parameters, such as the maximum growth rate (V max ), carrying capacity (K), and area under the curve (AUC), are calculated from absorbance values and used as proxies for fitness (Kugelberg et al 2005 ; Hansen et al 2007 ; Hegreness et al 2008 ; Paulander et al 2009 ; McDonald et al 2012 ; Ketola and Saarinen 2015 ; Kang et al 2019 ; Santiago et al 2020 ; Frey et al 2021 ). Populations with increased V max , K, or AUC values are considered to be more fit relative to those with lower values.…”

Section: Introductionmentioning

confidence: 99%

Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes

2023

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Following the completion of an adaptive evolution experiment, fitness evaluations are routinely conducted to assess the magnitude of adaptation. In doing so, proper consideration should be given when determining the appropriate methods as trade-offs may exist between accuracy and throughput. Here, we present three instances in which small changes in the framework or execution of fitness evaluations significantly impacted the outcomes. The first case illustrates that discrepancies in fitness conclusions can arise depending on the approach to evaluating fitness, the culture vessel used, and the sampling method. The second case reveals that variations in environmental conditions can occur associated with culture vessel material. Specifically, these subtle changes can greatly affect microbial physiology leading to changes in the culture pH and distorting fitness measurements. Finally, the last case reports that heterogeneity in CFU formation time can result in inaccurate fitness conclusions. Based on each case, considerations and recommendations are presented for future adaptive evolution experiments.

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Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method

Cited by 28 publications

References 18 publications

The CpG-dependent plant immune response to self-DNA triggers defence hormone signalling and improves fitness

The CpG-dependent plant immune response to self-DNA triggers defence hormone signalling and improves fitness

Limited Adaptation of Staphylococcus aureus during Transition from Colonization to Invasive Infection

Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes

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