“…It was associated with the origin of novel species (see details in the previous chapter). Initial environmental conditions promoted the origin of species possessing more and more complex genomes built combinatorically from relatively simple genomes of initial cells, as it was previously studied in [ 40 ]. We varied the time of initial phage invasion as well as its localization.…”
Section: Resultsmentioning
confidence: 99%
“…1 The hierarchical scheme of the HEC model (according to [ 35 , 38 ]) Fig. 2 Simulation of horizontal gene transfer in the HEC (according to [ 40 ]) …”
BackgroundBacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of (co)evolution in host-phage systems. Spatial (more generally, ecological) organization of the living environment is another factor affecting evolution. In this study, we have simulated and analyzed a series of computer models of microbial communities evolving in spatially distributed environments under the pressure of phage infection.ResultsWe modeled evolving microbial communities living in spatially distributed flowing environments. Non-specific nutrient supplied in the only spatial direction, resulting in its non-uniform distribution in environment. We varied the time and the location of initial phage infestation of cells as well as switched chemotaxis on and off. Simulations were performed with the Haploid evolutionary constructor software (http://evol-constructor.bionet.nsc.ru/).ConclusionSimulations have shown that the spatial location of initial phage invasion may lead to different evolutionary scenarios. Phage infection decreases the speciation rate by more than one order as far as intensified selection blocks the origin of novel viable populations/species, which could carve out potential ecological niches. The dependence of speciation rate on the invasion node location varied on the time of invasion. Speciation rate was found to be lower when the phage invaded fully formed community of sedentary cells (at middle and late times) at the species-rich regions. This is especially noticeable in the case of late-time invasion.Our simulation study has shown that phage infection affects evolution of microbial community slowing down speciation and stabilizing the system as a whole. This influencing varied in its efficiency depending on spatially-ecological factors as well as community state at the moment of phage invasion.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0620-4) contains supplementary material, which is available to authorized users.
“…It was associated with the origin of novel species (see details in the previous chapter). Initial environmental conditions promoted the origin of species possessing more and more complex genomes built combinatorically from relatively simple genomes of initial cells, as it was previously studied in [ 40 ]. We varied the time of initial phage invasion as well as its localization.…”
Section: Resultsmentioning
confidence: 99%
“…1 The hierarchical scheme of the HEC model (according to [ 35 , 38 ]) Fig. 2 Simulation of horizontal gene transfer in the HEC (according to [ 40 ]) …”
BackgroundBacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of (co)evolution in host-phage systems. Spatial (more generally, ecological) organization of the living environment is another factor affecting evolution. In this study, we have simulated and analyzed a series of computer models of microbial communities evolving in spatially distributed environments under the pressure of phage infection.ResultsWe modeled evolving microbial communities living in spatially distributed flowing environments. Non-specific nutrient supplied in the only spatial direction, resulting in its non-uniform distribution in environment. We varied the time and the location of initial phage infestation of cells as well as switched chemotaxis on and off. Simulations were performed with the Haploid evolutionary constructor software (http://evol-constructor.bionet.nsc.ru/).ConclusionSimulations have shown that the spatial location of initial phage invasion may lead to different evolutionary scenarios. Phage infection decreases the speciation rate by more than one order as far as intensified selection blocks the origin of novel viable populations/species, which could carve out potential ecological niches. The dependence of speciation rate on the invasion node location varied on the time of invasion. Speciation rate was found to be lower when the phage invaded fully formed community of sedentary cells (at middle and late times) at the species-rich regions. This is especially noticeable in the case of late-time invasion.Our simulation study has shown that phage infection affects evolution of microbial community slowing down speciation and stabilizing the system as a whole. This influencing varied in its efficiency depending on spatially-ecological factors as well as community state at the moment of phage invasion.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0620-4) contains supplementary material, which is available to authorized users.
“…In order to build and explore the multilevel model described above, the Haploid Evolutionary Constructor (HEC) software package was used [33,34]. Previously, HEC was used to model various aspects of the functioning and evolution of microbial communities: the balance between adaptability and biological diversity in symbiotic communities [35], evolutionary trends in the bacterial community-bacteriophage system [36,37], changes in genome complexity in prokaryotic populations [38], and the influence of the spatial organization of the community on the evolution of its constituent microorganisms [37,39].…”
The study focuses on the mechanisms of crossing the valleys of fitness by a population of haploid microorganisms, whose fitness depends on allelic values at two different loci and is determined by a complex landscape, the shape of which corresponds to the pattern "a mountain in the field surrounded by a trench"; these mechanisms are analyzed using computer modeling. We have studied the influence of various biological factors on the evolutionary perspective of microbial colonies, the reproduction rate of which is controlled by a protein consisting of two subunits encoded at different loci. Molecular genetic (mutation rate, affinity of subunits), population (fitness function landscape and population density), and ecological (concentration of available substrate in the habitat, flow intensity) factors have been considered. Our results demonstrate that the difference in fitness for various allelic combinations, while determining the shape of the fitness landscape, sets the optimal mutation rates to overcome its valleys and opens a window of opportunity for the evolution of the population toward the state of the highest average fitness. Moreover, depending on the fitness landscape type, either gradual or saltational evolutionary regimes are optimal for reaching the peak.
“…Было принято значение параметра k 1 (1), равное 0.01, что соответствует низкому штрафу за длину генома в соответствии с классификацией, используемой в статье [17].…”
Section: модель усложнения и упрощения метаболизма прокариот в прострunclassified
1 Институт цитологии и генетики СОРАН 2 Новосибирский национальный исследовательский государственный университет mat@bionet.nsc.ru Среди бактерий различных микробных сообществ существуют два противоположных эволюционных тренда -направленных на усложнение и на упрощение метаболизма. Как экосистемные ограничения, так и особенности генных сетей, лежащих в основе соответствующих метаболических процессов, выступают в качестве факторов, определяющих эволюционный исход в сообществе. В данной работе теоретически показано, что в пространственно-структурированных средах, характеризуемых наличием субстратных градиентов, возможно пространственное подразделение различных эволюционных тенденций в зависимости от близости ячейки к притоку питательных веществ, однако, эта закономерность разительно меняется для клеток, способных к активному движению в направлении хемоаттрактанта. Показано, что процессы горизонтального переноса и потери генов в сообществах подвижных прокариот могут приводить к стабильному распределению биомасс экогрупп, отличному от того, которое наблюдается в ходе естественного отбора в сообществе с полным набором комбинаций метаболических систем. Моделирование показало, что экологические паттерны самоорганизации микробных сообществ способствуют поддержанию различных стратегий, лежащих в основе сценариев, как усложнения, так и упрощения метаболизма. Таким образом, различные эволюционные тренды поддерживаются в средах с контрастными условиями, что обусловливается пространственной структурой местообитания.Ключевые слова: микробные сообщества, индивидуально-ориентированное моделирование, экологическое моделирование, эволюционное моделирование, пространственная гетерогенность.There are two evolutionary trends in genome organization among bacteria inhabiting microbial communitiestowards amplification and towards reduction of metabolism. Both environmental constraints and the complexity of underlying gene networks apparently act as factors determining evolutionary fate of a community. Here, we have theoretically shown that spatially structured habitats characterized by nutrient gradients allow subdivision of evolutionary trends depending on the distance of a sub-habitat to the nutrient source though this pattern changes drastically if cells are able to move actively towards chemo-attractant. We have demonstrated that horizontal gene transfer and gene loss occurring in the communities of motile bacteria are able to produce robust biomass dynamics of the ecogroups, which differs from the dynamics in the model of a community that consists of populations possessing all feasible metabolic combinations under natural selection. Simulations have shown that ecological patterns of self-organization of microbial communities cause sustainability of different strategies underlying the antagonistic evolutionary scenarios. Different evolutionary trends sustain in habitats with contrasting ecological conditions due to nutrient gradients that structure the environment spatially.
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