Long-term experimental evolution decouples size and production costs in Escherichia coli

High immigration rates critical for establishing emigration-driven diversity in microbial communities

Unraveling the mechanisms governing the diversity of ecological communities is a central goal in ecology. Although microbial dispersal constitutes an important ecological process, the effect of dispersal on microbial diversity is poorly understood. Here, we sought to fill this gap by combining a generalized Lotka-Volterra model with experimental investigations. Our model showed that emigration increases the diversity of the community when the immigration rate crosses a defined threshold, which we identified as Ineutral. We also found that at high immigration rates, emigration weakens the relative abundance of fast-growing species and thus enhances the mass effect and increases the diversity. We experimentally confirmed this finding using co-cultures of 20 bacterial strains isolated from the soil. Our model further showed that Ineutral decreases with the increase of species pool size, growth rate, and interspecies interaction. Our work deepens the understanding of the effects of dispersal on the diversity of natural communities.

Per capita sperm metabolism is density dependent

From bacteria to metazoans, higher density populations have lower per capita metabolic rates than lower density populations. The negative covariance between population density and metabolic rate is thought to represent a form of adaptive metabolic plasticity. A relationship between density and metabolism was actually first noted 100 years ago, and was focused on spermatozoa; even then, it was postulated that adaptive plasticity drove this pattern. Since then, contemporary studies of sperm metabolism specifically assume that sperm concentration has no effect on metabolism and that sperm metabolic rates show no adaptive plasticity. We did a systematic review to estimate the relationship between sperm aerobic metabolism and sperm concentration, for 198 estimates spanning 49 species, from protostomes to humans from 88 studies. We found strong evidence that per capita metabolic rates are concentration dependent: both within and among species, sperm have lower metabolisms in dense ejaculates, but increase their metabolism when diluted. On average, a 10-fold decrease in sperm concentration increased per capita metabolic rate by 35%. Metabolic plasticity in sperm appears to be an adaptive response, whereby sperm maximize their chances of encountering eggs.

On paradoxes between optimal growth, metabolic control analysis, and flux balance analysis

In Microbiology it is often assumed that growth rate is maximal. This may be taken to suggest that the dependence of the growth rate on every enzyme activity is at the top of an inverse-parabolic function, i.e. that all flux control coefficients should equal zero. This might seem to imply that the sum of these flux control coefficients equals zero. According to the summation law of Metabolic Control Analysis (MCA) the sum of flux control coefficients should equal 1 however. And in Flux Balance Analysis (FBA) catabolism is often limited by a hard bound, causing catabolism to fully control the fluxes, again in apparent contrast with a flux control coefficient of zero. Here we resolve these paradoxes (apparent contradictions) in an analysis that uses the 'Edinburgh pathway', the 'Amsterdam pathway', as well as a generic metabolic network providing the building blocks or Gibbs energy for microbial growth. We review and show that (i) optimization depends on so-called enzyme control coefficients rather than the 'catalytic control coefficients' of MCA's summation law, (ii) when optimization occurs at fixed total protein, the former differ from the latter to the extent that they may all become equal to zero in the optimum state, (iii) in more realistic scenarios of optimization where catalytically inert biomass is compensating or maintenance metabolism is taken into consideration, the optimum enzyme concentrations should not be expected to equal those that maximize the specific growth rate, (iv) optimization may be in terms of yield rather than specific growth rate, which resolves the paradox because the sum of catalytic control coefficients on yield equals 0, (v) FBA effectively maximizes growth yield, and for yield the summation law states 0 rather than 1, thereby removing the paradox, (vi) furthermore, FBA then comes more often to a 'hard optimum' defined by a maximum catabolic flux and a catabolic-enzyme control coefficient of 1. The trade-off between maintenance metabolism and growth is highlighted as worthy of further analysis.

Fertilization Mode Covaries with Body Size

AbstractThe evolution of internal fertilization has occurred repeatedly and independently across the tree of life. As it has evolved, internal fertilization has reshaped sexual selection and the covariances among sexual traits, such as testes size, and gamete traits. But it is unclear whether fertilization mode also shows evolutionary associations with traits other than primary sex traits. Theory predicts that fertilization mode and body size should covary, but formal tests with phylogenetic control are lacking. We used a phylogenetically controlled approach to test the covariance between fertilization mode and adult body size (while accounting for latitude, offspring size, and offspring developmental mode) among 1,232 species of marine invertebrates from three phyla. Within all phyla, external fertilizers are consistently larger than internal fertilizers: the consequences of fertilization mode extend to traits that are only indirectly related to reproduction. We suspect that other traits may also coevolve with fertilization mode in ways that remain unexplored.

Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming

Phytoplankton are responsible for half of all oxygen production and drive the ocean carbon cycle. Metabolic theory predicts that increasing global temperatures will cause phytoplankton to become more heterotrophic and smaller. Here, we uncover the metabolic trade-offs between cellular space, energy, and stress management driving phytoplankton thermal acclimation and how these might be overcome through evolutionary adaptation. We show that the observed relationships between traits such as chlorophyll, lipid content, C:N, and size can be predicted on the basis of the metabolic demands of the cell, the thermal dependency of transporters, and changes in membrane lipids. We suggest that many of the observed relationships are not fixed physiological constraints but rather can be altered through adaptation. For example, the evolution of lipid metabolism can favor larger cells with higher lipid content to mitigate oxidative stress. These results have implications for rates of carbon sequestration and export in a warmer ocean.

Copepod life history evolution under high- and low-food regimes

Copepods play a critical role in the carbon cycle of the planet - they mediate the sequestration of carbon into the deep ocean and are the trophic link between phytoplankton and marine food webs. Global change stressors that decrease copepod productivity create the potential for catastrophic positive feedback loops. Accordingly, a growing list of studies examine the evolutionary capacity of copepods to adapt to the two primary stressors associated with global change: warmer temperatures and lower pH. But the evolutionary capacity of copepods to adapt to changing food regimes, the third major stressor associated with global change, remains unknown. We used experimental evolution to explore how a 10-fold difference in food availability affects life history evolution in the copepod, Tisbe sp. over 2 years, and spanning 30+ generations. Different food regimes evoked evolutionary responses across the entire copepod life history: we observed evolution in body size, size-fecundity relationships and offspring investment strategies. Our results suggest that changes to food regimes reshape life histories and that cryptic evolution in traits such as body size is likely. We demonstrate that evolution in response to changes in ocean productivity will alter consumer life histories and may distort trophic links in marine foodchains. Evolution in response to changing phytoplankton productivity may alter the efficacy of the global carbon pump in ways that have not been anticipated until now.

Metabolic evolution in response to interspecific competition in a eukaryote

Competition drives rapid evolution, which, in turn, alters the trajectory of ecological communities. These eco-evolutionary dynamics are increasingly well-appreciated, but we lack a mechanistic framework for identifying the types of traits that will evolve and their trajectories. Metabolic theory offers explicit predictions for how competition should shape the (co)evolution of metabolism and size, but these are untested, particularly in eukaryotes. We use experimental evolution of a eukaryotic microalga to examine how metabolism, size, and demography coevolve under inter- and intraspecific competition. We find that the focal species evolves in accordance with the predictions of metabolic theory, reducing metabolic costs and maximizing population carrying capacity via changes in cell size. The smaller-evolved cells initially had lower population growth rates, as expected from their hyper-allometric metabolic scaling, but longer-term evolution yielded important departures from theory: we observed improvements in both population growth rate and carrying capacity. The evasion of this trade-off arose due to the rapid evolution of metabolic plasticity. Lineages exposed to competition evolved more labile metabolisms that tracked resource availability more effectively than lineages that were competition-free. That metabolic evolution can occur is unsurprising, but our finding that metabolic plasticity also co-evolves rapidly is new. Metabolic theory provides a powerful theoretical basis for predicting the eco-evolutionary responses to changing resource regimes driven by global change. Metabolic theory needs also to be updated to incorporate the effects of metabolic plasticity on the link between metabolism and demography, as this likely plays an underappreciated role in mediating eco-evolutionary dynamics of competition.

Rapamycin supplementation of Drosophila melanogaster larvae results in less viable adults with smaller cells

The intrinsic sources of mortality relate to the ability to meet the metabolic demands of tissue maintenance and repair, ultimately shaping ageing patterns. Anti-ageing mechanisms compete for resources with other functions, including those involved in maintaining functional plasma membranes. Consequently, organisms with smaller cells and more plasma membranes should devote more resources to membrane maintenance, leading to accelerated intrinsic mortality and ageing. To investigate this unexplored trade-off, we reared Drosophila melanogaster larvae on food with or without rapamycin (a TOR pathway inhibitor) to produce small- and large-celled adult flies, respectively, and measured their mortality rates. Males showed higher mortality than females. As expected, small-celled flies (rapamycin) showed higher mortality than their large-celled counterparts (control), but only in early adulthood. Contrary to predictions, the median lifespan was similar between the groups. Rapamycin administered to adults prolongs life; thus, the known direct physiological effects of rapamycin cannot explain our results. Instead, we invoke indirect effects of rapamycin, manifested as reduced cell size, as a driver of increased early mortality. We conclude that cell size differences between organisms and the associated burdens of plasma membrane maintenance costs may be important but overlooked factors influencing mortality patterns in nature.

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

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.

Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life-history trade-offs

Ecological theory predicts that early generation polyploids ('neopolyploids') should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested despite establishment being an intrinsically population-level process. We conducted population-level experiments where life-history investment in current and future growth was tracked in four lineage pairs of diploids and synthetic autotetraploids of the aquatic plant Spirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments. Although neopolyploid populations produce more biomass, they reach lower population sizes and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids. Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent seasons.

Comment on "Metabolic scaling is the product of life-history optimization"

The model used by White et al. (1) to explore life-history optimization of metabolic scaling has limited ability to capture observed combinations of growth and reproduction, including those of the domestic chicken. The analyses and interpretations may change substantially with realistic parameters. The model's biological and thermodynamic realism needs further exploration and justification before being applied to life-history optimization studies.

Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution

Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on their optical properties, morphology can be easily determined and tracked during experimental evolution. Furthermore, the directed evolution of new culturable morphological phenotypes can find use in synthetic biology to refine fermentation processes. It remains unknown whether and how fast we can obtain a stable mutant with distinct morphologies using fluorescence-activated cell sorting (FACS)-directed experimental evolution. Taking advantage of FACS and imaging flow cytometry (IFC), we direct the experimental evolution of the E. coli population undergoing continuous passage of sorted cells with specific optical properties. After ten rounds of sorting and culturing, a lineage with large cells resulting from incomplete closure of the division ring was obtained. Genome sequencing highlighted a stop-gain mutation in amiC, leading to a dysfunctional AmiC division protein. The combination of FACS-based selection with IFC analysis to track the evolution of the bacteria population in real-time holds promise to rapidly select and culture new morphologies and association tendencies with many potential applications.

Open problems in mathematical biology

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the extent to which our hypotheses agree with reality. But doing so in a systematic way is becoming increasingly challenging as our hypotheses become more detailed, and our data becomes more complex. Mathematical methods are therefore gaining in importance across the life- and biomedical sciences. Mathematical models allow us to test our understanding, make testable predictions about future behaviour, and gain insights into how we can control the behaviour of biological systems. It has been argued that mathematical methods can be of great benefit to biologists to make sense of data. But mathematics and mathematicians are set to benefit equally from considering the often bewildering complexity inherent to living systems. Here we present a small selection of open problems and challenges in mathematical biology. We have chosen these open problems because they are of both biological and mathematical interest.