scholarly journals Evolutionary Ecology of Natural Comammox Nitrospira Populations

mSystems ◽  
2022 ◽  
Author(s):  
Alejandro Palomo ◽  
Arnaud Dechesne ◽  
Otto X. Cordero ◽  
Barth F. Smets
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Single Species ◽  
Evolutionary Processes ◽  
Ecological Processes ◽  
Interacting Species ◽  
Microbial Species ◽  
Experimental Systems ◽  
Over Time

Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems.

scholarly journals Evolutionary ecology of natural comammox Nitrospira populations

2020 ◽  
Author(s):  
Alejandro Palomo ◽  
Arnaud Dechesne ◽  
Otto X. Cordero ◽  
Barth F. Smets
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Purifying Selection ◽  
Single Species ◽  
Species Interaction ◽  
Evolutionary Processes ◽  
Sand Filters ◽  
Experimental Systems ◽  
Stable Conditions ◽  
In The Wild

ABSTRACTMicrobial life on Earth commonly occurs in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during last decades, but most studies of evolutionary dynamics are based on single species in isolation or experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, favoured by low ammonium concentrations. Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. Nitrospira populations were separated by gene flow boundaries, suggesting natural and cohesive populations. They showed low homologous recombination and strong purifying selection, the latest process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. Additionally, we analysed evolutionary processes in populations from different habitats. Interestingly, our results suggest that in comammox Nitrospira these processes are not an intrinsic feature but greatly vary depending on the habitat they inhabit. Compared to other habitats, groundwater fed sand filters impose strong purifying selection and low recombination. Together, this study improves understanding of interactions and evolution of species in the wild, and sheds light on the environmental dependency of evolutionary processes.

scholarly journals Predicting ecosystem shifts requires new approaches that integrate the effects of climate change across entire systems

2011 ◽  
Vol 8 (2) ◽  
pp. 164-166 ◽  
Author(s):  
Bayden D. Russell ◽  
Christopher D. G. Harley ◽  
Thomas Wernberg ◽  
Nova Mieszkowska ◽  
Stephen Widdicombe ◽  
...  
Keyword(s):  
Climate Change ◽  
Life Stage ◽  
Experimental Studies ◽  
Single Species ◽  
Ecosystem Change ◽  
Energy Budgets ◽  
Ecological Change ◽  
Ecological Processes ◽  
Interacting Species ◽  
Climatic Impacts

Most studies that forecast the ecological consequences of climate change target a single species and a single life stage. Depending on climatic impacts on other life stages and on interacting species, however, the results from simple experiments may not translate into accurate predictions of future ecological change. Research needs to move beyond simple experimental studies and environmental envelope projections for single species towards identifying where ecosystem change is likely to occur and the drivers for this change. For this to happen, we advocate research directions that (i) identify the critical species within the target ecosystem, and the life stage(s) most susceptible to changing conditions and (ii) the key interactions between these species and components of their broader ecosystem. A combined approach using macroecology, experimentally derived data and modelling that incorporates energy budgets in life cycle models may identify critical abiotic conditions that disproportionately alter important ecological processes under forecasted climates.

scholarly journals Eco-evolutionary dynamics of social dilemmas

2016 ◽  
Author(s):  
Chaitanya S. Gokhale ◽  
Christoph Hauert
Keyword(s):  
Social Interactions ◽  
Evolutionary Dynamics ◽  
Complex Dynamics ◽  
Social Dilemmas ◽  
Microbial Populations ◽  
Evolutionary Processes ◽  
Ecological Processes ◽  
Evolutionary Trajectory ◽  
Changes Over Time ◽  
Better Than

AbstractSocial dilemmas are an integral part of social interactions. Cooperative actions, ranging from secreting extra-cellular products in microbial populations to donating blood in humans, are costly to the actor and hence create an incentive to shirk and avoid the costs. Nevertheless, cooperation is ubiquitous in nature. Both costs and benefits often depend non-linearly on the number and types of individuals involved–as captured by idioms such as ‘too many cooks spoil the broth’ where additional contributions are discounted, or ‘two heads are better than one’ where cooperators synergistically enhance the group benefit. Interaction group sizes may depend on the size of the population and hence on ecological processes. This results in feedback mechanisms between ecological and evolutionary processes, which jointly affect and determine the evolutionary trajectory. Only recently combined eco-evolutionary processes became experimentally tractable in microbial social dilemmas. Here we analyse the evolutionary dynamics of non-linear social dilemmas in settings where the population fluctuates in size and the environment changes over time. In particular, cooperation is often supported and maintained at high densities through ecological fluctuations. Moreover, we find that the combination of the two processes routinely reveals highly complex dynamics, which suggests common occurrence in nature.

scholarly journals Evolutionary ecology of microorganisms: from the tamed to the wild

2015 ◽  
Author(s):  
Jay T Lennon ◽  
Vincent J Denef
Keyword(s):  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Community Context ◽  
Ecological Processes ◽  
Rates Of Evolution ◽  
Ecological Principles ◽  
Managed Ecosystems ◽  
Microbial Systems ◽  
Empirical Approaches

An overarching goal of biology is to understand how evolutionary and ecological processes generate and maintain biodiversity. While evolutionary biologists interested in biodiversity tend to focus on the mechanisms controlling rates of evolution and how this influences the phylogenetic relationship among species, ecologists attempt to explain the distribution and abundance of taxa based upon interactions among species and their environment. Recently, a more concerted effort has been made to integrate some of the theoretical and empirical approaches from the fields of ecology and evolutionary biology. This integration has been motivated in part by the growing evidence that evolution can happen on “rapid” or contemporary time scales, suggesting that eco-evolutionary feedbacks can alter system dynamics in ways that cannot be predicted based on ecological principles alone. As such, it may be inappropriate to ignore evolutionary processes when attempting to understand ecological phenomena in natural and managed ecosystems. In this chapter, we highlight why it is particularly important to consider eco-evolutionary feedbacks for microbial populations. We emphasize some of the major processes that are thought to influence the strength of eco-evolutionary dynamics, provide an overview of methods used to quantify the relative importance of ecology and evolution, and showcase the importance of considering evolution in a community context and how this may influence the dynamics and stability of microbial systems under novel environmental conditions.

scholarly journals Evolutionary ecology of microorganisms: from the tamed to the wild

2015 ◽  
Author(s):  
Jay T Lennon ◽  
Vincent J Denef
Keyword(s):  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Community Context ◽  
Ecological Processes ◽  
Rates Of Evolution ◽  
Ecological Principles ◽  
Managed Ecosystems ◽  
Microbial Systems ◽  
Empirical Approaches

An overarching goal of biology is to understand how evolutionary and ecological processes generate and maintain biodiversity. While evolutionary biologists interested in biodiversity tend to focus on the mechanisms controlling rates of evolution and how this influences the phylogenetic relationship among species, ecologists attempt to explain the distribution and abundance of taxa based upon interactions among species and their environment. Recently, a more concerted effort has been made to integrate some of the theoretical and empirical approaches from the fields of ecology and evolutionary biology. This integration has been motivated in part by the growing evidence that evolution can happen on “rapid” or contemporary time scales, suggesting that eco-evolutionary feedbacks can alter system dynamics in ways that cannot be predicted based on ecological principles alone. As such, it may be inappropriate to ignore evolutionary processes when attempting to understand ecological phenomena in natural and managed ecosystems. In this chapter, we highlight why it is particularly important to consider eco-evolutionary feedbacks for microbial populations. We emphasize some of the major processes that are thought to influence the strength of eco-evolutionary dynamics, provide an overview of methods used to quantify the relative importance of ecology and evolution, and showcase the importance of considering evolution in a community context and how this may influence the dynamics and stability of microbial systems under novel environmental conditions.

Coevolution

Ecology ◽  
2013 ◽  
Author(s):  
Michael A. Brockhurst ◽  
Kayla C. King
Keyword(s):  
Historical Perspective ◽  
Evolutionary Dynamics ◽  
Evolutionary Change ◽  
Ecological Processes ◽  
Central Process ◽  
Biological Communities ◽  
Pattern And Process ◽  
Interacting Species ◽  
Evolutionary Force ◽  
Almost All

Coevolution, the reciprocal evolutionary change of ecologically interacting species, is a central process shaping the structure of biological communities and affects almost all organisms on earth. Its power as an evolutionary force arises from the often intense selection imposed by interactions between species, and from the fact that other species themselves evolve, thereby necessitating continual and sometimes rapid evolutionary change. The pattern and process of coevolution can be observed both at the microevolutionary (e.g., evolution of traits among populations) and macroevolutionary scales (e.g., generation of new species). From a microevolutionary perspective, coevolution can give rise to rapid evolutionary dynamics that may affect ecological processes; moreover, coevolution leads to the evolution of adaptations (and counter-adaptations) in interacting species and thereby may give rise to coadaptation of traits between species. Coevolution can drive divergent microevolutionary trajectories both within and between populations potentially leading to diversification and ultimately speciation. Thus, coevolution is a process linking microevolution and macroevolution. From a macroevolutionary perspective, tightly coevolving species may cospeciate such that the phylogenies of interacting clades appear congruent. This bibliography begins with a historical perspective, before considering conceptual issues surrounding coevolution and the debates that have shaped the field. The key publications exploring the pattern and process of coevolution at both microevolutionary and macroevolutionary scales are outlined.

Evolutionary Processes

2018 ◽  
Author(s):  
Stefan Thurner ◽  
Rudolf Hanel ◽  
Peter Klimekl
Keyword(s):  
Complex Systems ◽  
Power Law ◽  
Evolutionary Dynamics ◽  
Fitness Landscapes ◽  
Dynamical Process ◽  
Replicator Equation ◽  
Evolutionary Processes ◽  
Nk Model ◽  
Large Sets ◽  
Over Time

Evolutionary processes combine many features of complex systems: they are algorithmic; states co-evolve with interactions; they show power law statistics; they are selforganized critical; and they are driven non-equilibrium systems. Evolution is a dynamical process that changes the composition of large sets of interconnected elements, entities, or species over time. The essence of evolutionary processes is that, through the interaction of existing entities with each other and with their environment, they give rise to an open-ended process of creation and destruction of new entities. Evolutionary processes are critical, co-evolutionary, and combinatorial, meaning that thew entities are created from combinations of existing ones. We review the concepts of the replicator equation, fitness landscapes, cascading events, the adjacent possible. We review several classical quantitative approaches to evolutionary dynamics such as the NK model and the Bak–Snappen model. We propose a general and universal framework for evolutionary dynamics that is critical, co-evolutionary, and combinatorial.

scholarly journals Quantifying eco-evolutionary contributions to trait divergence in spatially structured systems

2019 ◽  
Author(s):  
Lynn Govaert ◽  
Jelena H. Pantel ◽  
Luc De Meester
Keyword(s):  
Genetic Differentiation ◽  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Temporal Dynamics ◽  
Similar Time ◽  
Spatial Studies ◽  
Trait Divergence ◽  
Structured Systems ◽  
Evolutionary Genetic ◽  
Over Time

AbstractEcological and evolutionary processes can occur at similar time scales, and hence influence one another. There has been much progress in the development of metrics that quantify contributions of ecological and evolutionary components to trait change over time. However, many empirical evolutionary ecology studies document genetic differentiation among populations structured in space. In both time and space, the observed differentiation in trait values among populations and communities can be the result of interactions between non-evolutionary (phenotypic plasticity, changes in the relative abundance of species) and evolutionary (genetic differentiation among populations) processes. However, the tools developed so far to quantify ecological and evolutionary contributions to trait change are implicitly addressing temporal dynamics because they require directionality of change from an ancestral to a derived state. Identifying directionality from one site to another in spatial studies of eco-evolutionary dynamics is not always possible and often not desired. We here suggest three modifications to existing metrics so they allow the partitioning of ecological and evolutionary contributions to changes in population and community trait values across landscapes. Applying these spatially modified metrics to published empirical examples shows how these metrics can be used to generate new empirical insights and to facilitate future comparative analyses. The possibility to apply eco-evolutionary partitioning metrics to populations and communities in real landscapes is critical as it will broaden our capacity to quantify eco-evolutionary interactions as they occur in nature.

scholarly journals Evolutionary ecology of microorganisms: from the tamed to the wild

2015 ◽  
Author(s):  
Jay T Lennon ◽  
Vincent J Denef
Keyword(s):  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Community Context ◽  
Ecological Processes ◽  
Rates Of Evolution ◽  
Ecological Principles ◽  
Managed Ecosystems ◽  
Microbial Systems ◽  
Empirical Approaches

An overarching goal of biology is to understand how evolutionary and ecological processes generate and maintain biodiversity. While evolutionary biologists interested in biodiversity tend to focus on the mechanisms controlling rates of evolution and how this influences the phylogenetic relationship among species, ecologists attempt to explain the distribution and abundance of taxa based upon interactions among species and their environment. Recently, a more concerted effort has been made to integrate some of the theoretical and empirical approaches from the fields of ecology and evolutionary biology. This integration has been motivated in part by the growing evidence that evolution can happen on “rapid” or contemporary time scales, suggesting that eco-evolutionary feedbacks can alter system dynamics in ways that cannot be predicted based on ecological principles alone. As such, it may be inappropriate to ignore evolutionary processes when attempting to understand ecological phenomena in natural and managed ecosystems. In this chapter, we highlight why it is particularly important to consider eco-evolutionary feedbacks for microbial populations. We emphasize some of the major processes that are thought to influence the strength of eco-evolutionary dynamics, provide an overview of methods used to quantify the relative importance of ecology and evolution, and showcase the importance of considering evolution in a community context and how this may influence the dynamics and stability of microbial systems under novel environmental conditions.

scholarly journals Alien Species vs. Native Species: From Community Ecology to Eco-Evolutionary Dynamics

2019 ◽  
Author(s):  
Andersonn Silveira Prestes
Keyword(s):  
Alien Species ◽  
Exotic Species ◽  
Native Species ◽  
Evolutionary Dynamics ◽  
Evolutionary Processes ◽  
Native Communities ◽  
Individualized Approach ◽  
History Of ◽  
Relationship Of ◽  
The Relationship

The establishment and spread of exotic species is a contemporary major concern. Alien species may become invasive in their new habitat, leading to both/either environmental and/or economic impacts. I briefly reviewed the literature in the last decade about the relationship of exotic species and native communities. I identified that professionals usually approach the subject in two main points of view: (1) researchers tend to point out the impacts of alien species on entire communities, evaluating if the relationship is positive, negative or neutral; (2) they focus on the eco-evolutionary processes involved in the introductions, the dynamics of invasion, and individual study cases. When evaluating the response of introductions to entire communities, evidence seems to be ambiguous and may support positive, negative or neutral relationship, especially depending on the scale approached. The unique eco-evolutionary pathways of each introduction may be a great shortcoming in the searching for generalities. On the other hand, advances have been made in understanding the dynamics of invasion on different lineages through a more selective/individualized approach. I suggest that the dynamics of invasion might be studied through a perspective in which different eco-evolutionary processes, levels of organization (from gene to entire communities), the history of the organism(s) and time are taken into account. Individual cases might be compared in attempt to understand how the relationship exotic and native works and in the search for generalities.

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