Fast eco-evolutionary changes in bacterial genomes after anthropogenic perturbation

Abstract

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...

Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation

“…We also thank Dr. Erika Aguirre Planter and Dr. Laura Espinosa-Asuar for the technical support. This manuscript was released as a pre-print at bioRxiv ( García-Ulloa et al, 2020 ).…”