The significance of nitrogen cost minimization in proteomes of marine microorganisms

Marine microorganisms thrive under low levels of nitrogen (N). N cost minimization is a major selective pressure imprinted on open-ocean microorganism genomes. Here we show that amino-acid sequences from the open ocean are reduced in N, but increased in average mass compared with coastal-ocean microorganisms. Nutrient limitation exerts significant pressure on organisms supporting the trade-off between N cost minimization and increased average mass of amino acids that is a function of increased A+T codon usage. N cost minimization, especially of highly expressed proteins, reduces the total cellular N budget by 2.7–10% this minimization in combination with reduction in genome size and cell size is an evolutionary adaptation to nutrient limitation. The biogeochemical and evolutionary precedent for these findings suggests that N limitation is a stronger selective force in the ocean than biosynthetic costs and is an important evolutionary strategy in resource-limited ecosystems.     

Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus

Rapid adaptation can prevent extinction when populations are exposed to extremely marginal or stressful environments. Factors that affect the likelihood of evolutionary rescue from extinction have been identified, but much less is known about the evolutionary dynamics (e.g., rates and patterns of allele frequency change) and genomic basis of successful rescue, particularly in multicellular organisms. We conducted an evolve‐and‐resequence experiment to investigate the dynamics of evolutionary rescue at the genetic level in the cowpea seed beetle, Callosobruchus maculatus, when it is experimentally shifted to a stressful host plant, lentil. Low survival (~1%) at the onset of the experiment caused population decline. But adaptive evolution quickly rescued the population, with survival rates climbing to 69% by the F5 generation and 90% by the F10 generation. Population genomic data showed that rescue likely was caused by rapid evolutionary change at multiple loci, with many alleles fixing or nearly fixing within five generations of selection on lentil. Selection on these loci was only moderately consistent in time, but parallel evolutionary changes were evident in sublines formed after the lentil line had passed through a bottleneck. By comparing estimates of selection and genomic change on lentil across five independent C. maculatus lines (the new lentil‐adapted line, three long‐established lines and one case of failed evolutionary rescue), we found that adaptation on lentil occurred via somewhat idiosyncratic evolutionary changes. Overall, our results suggest that evolutionary rescue in this system can be caused by very strong selection on multiple loci driving rapid and pronounced genomic change.     

Predicting vegetation type through physiological and environmental interactions with leaf traits: evergreen and deciduous forests in an earth system modeling framework

Earth system models are incorporating plant trait diversity into their land components to better predict vegetation dynamics in a changing climate. However, extant plant trait distributions will not allow extrapolations to novel community assemblages in future climates, which will require a mechanistic understanding of the trade‐offs that determine trait diversity. In this study, we show how physiological trade‐offs involving leaf mass per unit area (LMA), leaf lifespan, leaf nitrogen, and leaf respiration may explain the distribution patterns of evergreen and deciduous trees in the temperate and boreal zones based on (1) an evolutionary analysis of a simple mathematical model and (2) simulation experiments of an individual‐based dynamic vegetation model (i.e., LM3‐PPA). The evolutionary analysis shows that these leaf traits set up a trade‐off between carbon‐ and nitrogen‐use efficiency at the scale of individual trees and therefore determine competitively dominant leaf strategies. As soil nitrogen availability increases, the dominant leaf strategy switches from one that is high in nitrogen‐use efficiency to one that is high in carbon‐use efficiency or, equivalently, from high‐LMA/long‐lived leaves (i.e., evergreen) to low‐LMA/short‐lived leaves (i.e., deciduous). In a region of intermediate soil nitrogen availability, the dominant leaf strategy may be either deciduous or evergreen depending on the initial conditions of plant trait abundance (i.e., founder controlled) due to feedbacks of leaf traits on soil nitrogen mineralization through litter quality. Simulated successional patterns by LM3‐PPA from the leaf physiological trade‐offs are consistent with observed successional dynamics of evergreen and deciduous forests at three sites spanning the temperate to boreal zones.     

Nitrogen availability to Pseudomonas fluorescens DF57 is limited during decomposition of barley straw in bulk soil and in the barley rhizosphere.

The availability of nitrogen to Pseudomonas fluorescens DF57 during straw degradation in bulk soil and in barley rhizosphere was studied by introducing a bioluminescent reporter strain (DF57-N3), responding to nitrogen limitation, to model systems of varying complexity. DF57-N3 was apparently not nitrogen limited in the natural and sterilized bulk soil used for these experiments. The soil was subsequently amended with barley straw, representing a plant residue with a high carbon-to-nitrogen ratio (between 60 and 100). In these systems the DF57-N3 population gradually developed a nitrogen limitation response during the first week of straw decomposition, but exclusively in the presence of the indigenous microbial population. This probably reflects the restricted ability of DF57 to degrade plant polymers by hydrolytic enzymes. The impact of the indigenous population on nitrogen availability to DF57-N3 was mimicked by the cellulolytic organism Trichoderma harzianum Rifai strain T3 when coinoculated with DF57-N3 in sterilized, straw-amended soil. Limitation occurred concomitantly with fungal cellulase production, pointing to the significance of hydrolytic activity for the mobilization of straw carbon sources, thereby increasing the nitrogen demand. Enhanced survival of DF57-N3 in natural soil after straw amendment further indicated that DF57 was cross-fed with carbon/energy sources. The natural barley rhizosphere was experienced by DF57-N3 as an environment with restricted nitrogen availability regardless of straw amendment. In the rhizosphere of plants grown in sterilized soil, nitrogen limitation was less severe, pointing to competition with indigenous microorganisms as an important determinant of the nitrogen status for DF57-N3 in this environment. Hence, these studies have demonstrated that nitrogen availability and gene expression in Pseudomonas is intimately linked to the structure and function of the microbial community. Further, it was demonstrated that the activities of cellulolytic microorganisms may affect the availability of energy and specific nutrients to a group of organisms deficient in hydrolytic enzyme activities.     

Nitrogen Availability to Pseudomonas fluorescens DF57 Is Limited during Decomposition of Barley Straw in Bulk Soil and in the Barley Rhizosphere

The availability of nitrogen to Pseudomonas fluorescens DF57 during straw degradation in bulk soil and in barley rhizosphere was studied by introducing a bioluminescent reporter strain (DF57-N3), responding to nitrogen limitation, to model systems of varying complexity. DF57-N3 was apparently not nitrogen limited in the natural and sterilized bulk soil used for these experiments. The soil was subsequently amended with barley straw, representing a plant residue with a high carbon-to-nitrogen ratio (between 60 and 100). In these systems the DF57-N3 population gradually developed a nitrogen limitation response during the first week of straw decomposition, but exclusively in the presence of the indigenous microbial population. This probably reflects the restricted ability of DF57 to degrade plant polymers by hydrolytic enzymes. The impact of the indigenous population on nitrogen availability to DF57-N3 was mimicked by the cellulolytic organism Trichoderma harzianum Rifai strain T3 when coinoculated with DF57-N3 in sterilized, straw-amended soil. Limitation occurred concomitantly with fungal cellulase production, pointing to the significance of hydrolytic activity for the mobilization of straw carbon sources, thereby increasing the nitrogen demand. Enhanced survival of DF57-N3 in natural soil after straw amendment further indicated that DF57 was cross-fed with carbon/energy sources. The natural barley rhizosphere was experienced by DF57-N3 as an environment with restricted nitrogen availability regardless of straw amendment. In the rhizosphere of plants grown in sterilized soil, nitrogen limitation was less severe, pointing to competition with indigenous microorganisms as an important determinant of the nitrogen status for DF57-N3 in this environment. Hence, these studies have demonstrated that nitrogen availability and gene expression in Pseudomonas is intimately linked to the structure and function of the microbial community. Further, it was demonstrated that the activities of cellulolytic microorganisms may affect the availability of energy and specific nutrients to a group of organisms deficient in hydrolytic enzyme activities.     

Evolutionary dynamics of the leaf phenological cycle in an oak metapopulation along an elevation gradient

It has been predicted that environmental changes will radically alter the selective pressures on phenological traits. Long‐lived species, such as trees, will be particularly affected, as they may need to undergo major adaptive change over only one or a few generations. The traits describing the annual life cycle of trees are generally highly evolvable, but nothing is known about the strength of their genetic correlations. Tight correlations can impose strong evolutionary constraints, potentially hampering the adaptation of multivariate phenological phenotypes. In this study, we investigated the evolutionary, genetic and environmental components of the timing of leaf unfolding and senescence within an oak metapopulation along an elevation gradient. Population divergence, estimated from in situ and common‐garden data, was compared to expectations under neutral evolution, based on microsatellite markers. This approach made it possible (1) to evaluate the influence of genetic correlation on multivariate local adaptation to elevation and (2) to identify traits probably exposed to past selective pressures due to the colder climate at high elevation. The genetic correlation was positive but very weak, indicating that genetic constraints did not shape the local adaptation pattern for leaf phenology. Both spring and fall (leaf unfolding and senescence, respectively) phenology timings were involved in local adaptation, but leaf unfolding was probably the trait most exposed to climate change‐induced selection. Our data indicated that genetic variation makes a much smaller contribution to adaptation than the considerable plastic variation displayed by a tree during its lifetime. The evolutionary potential of leaf phenology is, therefore, probably not the most critical aspect for short‐term population survival in a changing climate.     

Local adaptation,dispersal evolution,and the spatial eco‐evolutionary dynamics of invasion

Local adaptation and dispersal evolution are key evolutionary processes shaping the invasion dynamics of populations colonizing new environments. Yet their interaction is largely unresolved. Using a single‐species population model along a one‐dimensional environmental gradient, we show how local competition and dispersal jointly shape the eco‐evolutionary dynamics and speed of invasion. From a focal introduction site, the generic pattern predicted by our model features a temporal transition from wave‐like to pulsed invasion. Each regime is driven primarily by local adaptation, while the transition is caused by eco‐evolutionary feedbacks mediated by dispersal. The interaction range and cost of dispersal arise as key factors of the duration and speed of each phase. Our results demonstrate that spatial eco‐evolutionary feedbacks along environmental gradients can drive strong temporal variation in the rate and structure of population spread, and must be considered to better understand and forecast invasion rates and range dynamics.     

Rapid evolution towards heavy metal resistance by mountain birch around two subarctic copper-nickel smelters

Adaptations to pollution among long‐lived trees have rarely been documented, possibly because of their long reproductive cycles and the evolutionarily short timescales of anthropogenic pollution. Here, I present the results of a greenhouse experiment that suggest rapid evolutionary adaptation of mountain birch [Betula pubescens subsp. czerepanovii (Orlova) Hämet‐Ahti] to heavy metal (HM) stress around two copper–nickel smelters in NW Russia. The adaptation incurs a cost with reduced performance of adapted seedlings in pristine conditions. The industrial barrens around the studied smelters are extremely high‐stress sites with low seed germination and survival. It is likely that strong natural selection has eliminated all sensitive genotypes within one or two generations, with only the most tolerant individuals persisting and producing adapted seeds in the individual barrens. The results were similar from around both smelters, suggesting parallel evolution towards HM resistance.     

How phenotypic convergence arises in experimental evolution

Evolutionary convergence is a core issue in the study of adaptive evolution, as well as a highly debated topic at present. Few studies have analyzed this issue using a “real‐time” or evolutionary trajectory approach. Do populations that are initially differentiated converge to a similar adaptive state when experiencing a common novel environment? Drosophila subobscura populations founded from different locations and years showed initial differences and variation in evolutionary rates in several traits during short‐term (～20 generations) laboratory adaptation. Here, we extend that analysis to 40 more generations to analyze (1) how differences in evolutionary dynamics among populations change between shorter and longer time spans, and (2) whether evolutionary convergence occurs after 60 generations of evolution in a common environment. We found substantial variation in longer term evolutionary trajectories and differences between short‐ and longer term evolutionary dynamics. Although we observed pervasive patterns of convergence toward the character values of long‐established populations, populations still remain differentiated for several traits at the final generations analyzed. This pattern might involve transient divergence, as we report in some cases, indicating that more generations should lead to final convergence. These findings highlight the importance of longer term studies for understanding convergent evolution.     

Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton

Understanding the mechanisms that determine how phytoplankton adapt to warming will substantially improve the realism of models describing ecological and biogeochemical effects of climate change. Here, we quantify the evolution of elevated thermal tolerance in the phytoplankton, Chlorella vulgaris. Initially, population growth was limited at higher temperatures because respiration was more sensitive to temperature than photosynthesis meaning less carbon was available for growth. Tolerance to high temperature evolved after ≈ 100 generations via greater down‐regulation of respiration relative to photosynthesis. By down‐regulating respiration, phytoplankton overcame the metabolic constraint imposed by the greater temperature sensitivity of respiration and more efficiently allocated fixed carbon to growth. Rapid evolution of carbon‐use efficiency provides a potentially general mechanism for thermal adaptation in phytoplankton and implies that evolutionary responses in phytoplankton will modify biogeochemical cycles and hence food web structure and function under warming. Models of climate futures that ignore adaptation would usefully be revisited.     

Stoichiometric regulation of phytoplankton toxins

Ecological Stoichiometry theory predicts that the production, elemental structure and cellular content of biomolecules should depend on the relative availability of resources and the elemental composition of their producer organism. We review the extent to which carbon‐ and nitrogen‐rich phytoplankton toxins are regulated by nutrient limitation and cellular stoichiometry. Consistent with theory, we show that nitrogen limitation causes a reduction in the cellular quota of nitrogen‐rich toxins, while phosphorus limitation causes an increase in the most nitrogen‐rich paralytic shellfish poisoning toxin. In addition, we show that the cellular content of nitrogen‐rich toxins increases with increasing cellular N : P ratios. Also consistent with theory, limitation by either nitrogen or phosphorus promotes the C‐rich toxin cell quota or toxicity of phytoplankton cells. These observed relationships may assist in predicting and managing toxin‐producing phytoplankton blooms. Such a stoichiometric regulation of toxins is likely not restricted to phytoplankton, and may well apply to carbon‐ and nitrogen‐rich secondary metabolites produced by bacteria, fungi and plants.     

Spatiotemporal variation in local adaptation of a specialist insect herbivore to its long‐lived host plant

Local adaptation of interacting species to one another indicates geographically variable reciprocal selection. This process of adaptation is central in the organization and maintenance of genetic variation across populations. Given that the strength of selection and responses to it often vary in time and space, the strength of local adaptation should in theory vary between generations and among populations. However, such spatiotemporal variation has rarely been explicitly demonstrated in nature and local adaptation is commonly considered to be relatively static. We report persistent local adaptation of the short‐lived herbivore Abrostola asclepiadis to its long‐lived host plant Vincetoxicum hirundinaria over three successive generations in two studied populations and considerable temporal variation in local adaptation in six populations supporting the geographic mosaic theory. The observed variation in local adaptation among populations was best explained by geographic distance and population isolation, suggesting that gene flow reduces local adaptation. Changes in herbivore population size did not conclusively explain temporal variation in local adaptation. Our results also imply that short‐term studies are likely to capture only a part of the existing variation in local adaptation.     

Constraints on adaptation of Escherichia coli to mixed‐resource environments increase over time

Can a population evolved in two resources reach the same fitness in both as specialist populations evolved in each of the individual resources? This question is central to theories of ecological specialization, the maintenance of genetic variation, and sympatric speciation, yet relatively few experiments have examined costs of generalism over long‐term adaptation. We tested whether selection in environments containing two resources limits a population's ability to adapt to the individual resources by comparing the fitness of replicate Escherichia coli populations evolved for 6000 generations in the presence of glucose or lactose alone (specialists), or in varying presentations of glucose and lactose together (generalists). We found that all populations had significant fitness increases in both resources, though the magnitude and rate of these increases differed. For the first 4000 generations, most generalist populations increased in fitness as quickly in the individual resources as the corresponding specialist populations. From 5000 generations, however, a widespread cost of adaptation affected all generalists, indicating a growing constraint on their abilities to adapt to two resources simultaneously. Our results indicate that costs of generalism are prevalent, but may influence evolutionary trajectories only after a period of cost‐free adaptation.     

Rate of resistance evolution and polymorphism in long‐ and short‐lived hosts

Recent theoretical work has shown that long‐lived hosts are expected to evolve higher equilibrium levels of disease resistance than shorter‐lived hosts, but questions of how longevity affects the rate of resistance evolution and the maintenance of polymorphism remain unanswered. Conventional wisdom suggests that adaptive evolution should occur more slowly in long‐lived organisms than in short‐lived organisms. However, the opposite may be true for the evolution of disease‐resistance traits where exposure to disease, and therefore the strength of selection for resistance increases with longevity. In a single locus model of innate resistance to a frequency‐dependent, sterilizing disease, longer lived hosts evolved resistance more rapidly than short‐lived hosts. Moreover, resistance in long‐lived hosts could only be polymorphic for more costly and more extreme resistance levels than short‐lived hosts. The increased rate of evolution occurred in spite of longer generation times because longer‐lived hosts had both a longer period of exposure to disease as well as higher disease prevalence. Qualitatively similar results were found when the model was extended to mortality‐inducing diseases, or to density‐dependent transmission modes. Our study shows that the evolutionary dynamics of host resistance is determined by more than just levels of resistance and cost, but is highly sensitive to the life‐history traits of the host.     

From nature to the laboratory: the impact of founder effects on adaptation

Most founding events entail a reduction in population size, which in turn leads to genetic drift effects that can deplete alleles. Besides reducing neutral genetic variability, founder effects can in principle shift additive genetic variance for phenotypes that underlie fitness. This could then lead to different rates of adaptation among populations that have undergone a population size bottleneck as well as an environmental change, even when these populations have a common evolutionary history. Thus, theory suggests that there should be an association between observable genetic variability for both neutral markers and phenotypes related to fitness. Here, we test this scenario by monitoring the early evolutionary dynamics of six laboratory foundations derived from founders taken from the same source natural population of Drosophila subobscura. Each foundation was in turn three‐fold replicated. During their first few generations, these six foundations showed an abrupt increase in their genetic differentiation, within and between foundations. The eighteen populations that were monitored also differed in their patterns of phenotypic adaptation according to their immediately ancestral founding sample. Differences in early genetic variability and in effective population size were found to predict differences in the rate of adaptation during the first 21 generations of laboratory evolution. We show that evolution in a novel environment is strongly contingent not only on the initial composition of a newly founded population but also on the stochastic changes that occur during the first generations of colonization. Such effects make laboratory populations poor guides to the evolutionary genetic properties of their ancestral wild populations.     

Genetic and demographic founder effects have long‐term fitness consequences for colonising populations

Colonisation is a fundamental ecological and evolutionary process that drives the distribution and abundance of organisms. The initial ability of colonists to establish is determined largely by the number of founders and their genetic background. We explore the importance of these demographic and genetic properties for longer term persistence and adaptation of populations colonising a novel habitat using experimental populations of Tribolium castaneum. We introduced individuals from three genetic backgrounds (inbred – outbred) into a novel environment at three founding sizes (2–32), and tracked populations for seven generations. Inbreeding had negative effects, whereas outbreeding generally had positive effects on establishment, population growth and long‐term persistence. Severe bottlenecks due to small founding sizes reduced genetic variation and fitness but did not prevent adaptation if the founders originated from genetically diverse populations. Thus, we find important and largely independent roles for both demographic and genetic processes in driving colonisation success.     

Contrasting mechanisms of proteomic nitrogen thrift in Prochlorococcus

Organisms limited by carbon, nitrogen or sulphur can reduce protein production costs by transitions to less costly amino acids, or by reducing protein expression. These alternative mechanisms of nutrient thrift might respond differently to selection, but this possibility remains untested. We hypothesized that relatively invariant sequence composition responds to long-term variation in nutrient concentrations, whereas dynamic expression profiles vary with nutrient predictability. Prolonged nutrient scarcity favours proteome-wide nutrient reduction. Under stable, nonfluctuating nutrient availability, reduction of nutrient content typically occurs in proteins upregulated when nutrient availability is low, e.g. assimilation and catabolism. We suggest that fluctuating nutrient availability favours mechanisms involving short-term downregulation of nutrient-rich proteins. We analysed protein nitrogen content in six high-light, low-nutrient adapted (HL) vs. six low-light, high-nutrient adapted (LL) Prochlorococcus (marine cyanobacteria) strains, alongside expression data under experimental nitrogen and phosphorus limitation in two strains, MED4 (HL) vs. MIT9313 (LL). HL strains contained less nitrogen, but DNA GC content confounded this relationship. While anabolic and catabolic proteins had normal nitrogen content, most strains showed reduced nitrogen in typical nitrogen stress response proteins. In the experimental data set, though, proteins upregulated under nitrogen limitation were nitrogen-poor only in MIT9313, not MED4. MIT9313 responded similarly to nitrogen and phosphorus limitation, with slow, sustained downregulation of nitrogen-rich ribosomal proteins. In contrast, under nitrogen but not phosphorus limitation, MED4 rapidly downregulated ribosomal proteins. MED4's specific, rapid nitrogen response suggests adaptation to fluctuating conditions, supporting previous work. Thus, we identify contrasting proteomic nitrogen thrift mechanisms within Prochlorococcus consistent with different nutrient regimes.