Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

Avitia, Morena; Escalante, Ana E.; Rebollar, Eria A.; Moreno‐Letelier, Alejandra; Eguiarte, Luis E.; Souza, Valeria

doi:10.7717/peerj.696

Cited by 16 publications

(28 citation statements)

References 64 publications

(90 reference statements)

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“…However, in that case, the outcome could be easier to predict, given the possible black queen dynamics [82] in B. coahuilensis, which was a specialized lineage with a particularly small genome, lacking several metabolic pathways, therefore, an organism highly dependent on several metabolites from other community members [30,81,83]. What was observed in our study is more intriguing, since P. otitidis is a planktonic generalist that was observed consistently over the years at Churince [43–45, 33, 35, 36] and even experimented a dramatic population increase just before apparently going locally extinct.…”

Section: Discussionmentioning

confidence: 69%

“…Coalescent simulations were performed using the observed allele frequency spectrum of the Pseudomonas otitidis population from 2015, taking into account an initial population range of 500,000 - 8,000,000 estimated by Avitia et al [45], mutation rate of wild type P. aeruginosa of 5e-9 calculated by Oliver et al [64], generational time of P. aeruginosa in low phosphorus medium of 0.04 h-1 calculated by Buch et al [63], and range of generations from 2003 to 2015 of 6300 to 2100 and recombination rate (R) from R/θ = 2.5 e-8 calculated in this study. The solid colored lines are the average values and the shaded areas represent the 95% confidence intervals.…”

Section: Resultsmentioning

confidence: 99%

“…Seven colonies of October 2015 were identified as P. otitidis through a blast search against the RefSeq database. Additionally, five isolates from August 2003 previously identified as P. otitidis [45] were used for the analysis as representatives of the undisturbed state of the lagoon.…”

Section: Methodsmentioning

confidence: 99%

“…Demographic models allow the possibility of positive (expansion: E) and negative (contraction: K) population changes as well as absence of changes (constant population size: C) in three time intervals (August 2003 to October 2011; October 2011 to November 2012; November 2012 to October 2015) resulting in 27 different models. The initial parameters used in the models were: generational time of P. aeruginosa in low phosphorus medium = 0.04 h-1 [63], range of generations from 2003 to 2015 = 6300 to 2100 (this study), mutation rate of P. aeruginosa wild type = 5 e-9 [64], recombination rate calculated from R/θ = 2.5 e-8 (this study), effective population size range = 500,000 to 8,000,000 [45]. The evaluation of the models was done by calculating and comparing their weighted AIC values (wAIC) which serve as a measure of the strength of each model in comparison to the others, given their likelihoods, from 0 to 100%.…”

Section: Methodsmentioning

confidence: 99%

“…Biology and ecology of pseudomonads from Churince has been described in different studies [35, 43–45], and more recently two new strains of the P. aeruginosa PA14 clade native to Laguna Intermedia were sampled during the first desiccation event in 2011 [36]. P. otitidis from CCB represented a separate native lineage that was present, but was rare, before the perturbations at Laguna Intermedia [44].…”

Section: Introductionmentioning

confidence: 99%

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Fast eco-evolutionary changes in bacterial genomes after anthropogenic perturbation

García-Ulloa

et al. 2020

Preprint

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22Anthropogenic perturbations such as water overexploitation introduce novel 23 selective pressures to the natural environments, impacting on the genomic 24 variability of organisms and thus altering the evolutionary trajectory of its 25 populations. Bad agricultural practices and defective policies in Cuatro Cienegas, 26 Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire 27 hydrological systems to the brink of extinction together with their native 28 populations. Here, we studied the effects of continuous water overexploitation on 29 an environmental aquatic lineage of Pseudomonas otitidis, inhabitant to a 30 particularly affected lagoon of an exhaustively studied system in the middle of the 31 desert, over a 13 year period which encompasses three desiccation events. By 32 comparing the genomes of a population sample from 2003 (original state) and 33 2015 (perturbed state), we analyzed the demographic history and evolutionary 34 response of this bacterial lineage to the perturbation. Through coalescent 35 simulations, we obtained a demographic model of contraction-expansion-36 contraction which, alongside an increment in mean Tajima's D and recombination 37 rate, loss of genetic and nucleotidic variation and a single amino acid under 38 positive selection, points the occurrence of an evolutionary rescue event, possibly 39 potentiated by horizontal gene transfer, where the population nearly went extinct 40 during the first desiccation event but sharply recovered in the second and adapted 41 to its new environment. Furthermore, the gain of phosphorylation, DNA 42 recombination and small-molecule metabolism and loss of biosynthetic and 43 regulation genes on the exclusive accessory genome suggest a functional shift to a 3 44 more generalist scavenger lifestyle in an environment that went from oligotrophic to 45 nutrient-rich. Human population growth and human activities have negatively impacted fresh-64 water bodies globally [1,2]. It is estimated that the water demand for human 65 activities exceeds climate change as the most important factor influencing the state 66 of water systems [3]. Among the different human uses for freshwater, agriculture is 67 responsible for 70% of the global water extraction, a figure that may increase to 68 90% by 2050 due to drought and warmer temperatures associated with climate 69 change [4,5]. This negative feedback between diminishing fresh-water stocks, 70 deforestation and climate change, has already caused droughts and desiccation 71 events worldwide which in turn generate fragmentation and loss of habitat, putting 72 the survival of many wild species at stake [6-8] 73 These extreme events caused by anthropogenic perturbations introduce 74 novel and strong selective pressures; the response to these pressures depends on 75 the standing genetic variation within populations [9]. In many cases, the lack of 76 capability to adapt to the new environments impacts entire communities and 77 ecosystems [10]. This "domino" effect is the reflection of the ti...

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