Plasticity predicts evolution in a marine alga

Unveiling the Anti-Aging Potential of Marine Natural Bioproducts

Aging is a natural process resulting in the progressive impairment of multiple functions in the human body, leading to a decline in cellular functionality and the development of aging-related diseases. External stress factors, such as ultraviolet (UV) radiation, pollution, and toxin exposure, increase oxidative stress, damage cellular repair mechanisms, and speed up aging processes. With the rise in the world's aging population, there are enlarged demands for the use of sustainable natural products in food, nutrient supplements and cosmetics that can slow down aging and prolong healthy life and longevity. Algae, including both macroalgae and microalgae, have been recognised as a source of valuable proteins, amino acids, fatty acids, vitamins, and minerals useful for human consumption and medical applications. With increasing demands for nutraceutical and pharmaceutical bioproducts from environmentally friendly resources, the biotechnological industry, over recent decades, has had to provide new, advanced solutions using modern high-throughput omics technologies. The application of proteomics in the area of discoveries of natural products with anti-aging properties has become more popular for wide industry applications. New proteomics profiling provides a better understanding of changes occurring in protein and peptide content, their structure, function and interactions, as well as the regulatory processes and molecular pathways. Mass spectrometry-based proteomics has been used for a wide range of applications including protein identification, characterisation, as well as quantification of proteins within the proteome and sub-proteome. The application of chemical proteomics facilitated the identification of natural products approach and included the synthesis of probes and target fishing, allowing the advanced identification of proteins of interest. This review focuses on marine macro- and microalgal anti-aging compounds and novel proteomics approaches, providing recent experimental evidence of their involvement in anti-aging processes that should facilitate their use in innovative approaches and sustainable biotechnological applications.

Inorganic Carbon Acquisition and Photosynthetic Metabolism in Marine Photoautotrophs: A Summary

The diffusive availability of CO2 for photosynthesis is orders of magnitude lower in water than in air. This, and the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) for CO2, implies that most marine photoautotrophs (cyanobacteria, microalgae, macroalgae and marine angiosperms or seagrasses) would be severely restricted were they to rely only on dissolved CO2 for their photosynthetic performance. On the other hand, the ~120 times higher concentration of bicarbonate (HCO3-) makes this inorganic carbon (Ci) form more available for utilisation by marine photosynthesisers. The most common way in marine macrophytes to utilise HCO3- is to convert it to CO2 within acidic micro-zones of diffusion boundary layers (DBLs), including the cell walls, as catalysed by an outwardly acting carbonic anhydrase (CA). This would then generate an intra-chloroplastic (or for cyanobacteria intra-carboxysomal) CO2-concentrating mechanism (CCM). Some algae (e.g., the common macroalgae Ulva spp.) and most cyanobacteria and microalgae feature direct HCO3- uptake as the most efficient CCM, while others (e.g., some red algae growing under low-light conditions) may rely on CO2 diffusion only. We will in this contribution summarise our current understanding of photosynthetic carbon assimilation of submerged marine photoautotrophs, and in particular how their 'biophysical' CCMs differ from the 'biochemical' CCMs of terrestrial C4 and Crassulacean Acid Metabolism (CAM) plants (for which there is very limited evidence in cyanobacteria, algae and seagrasses).

Trait and plasticity evolution under competition and mutualism in evolving pairwise yeast communities

Although we have a good understanding of how phenotypic plasticity evolves in response to abiotic environments, we know comparatively less about responses to biotic interactions. We experimentally tested how competition and mutualism affected trait and plasticity evolution of pairwise communities of genetically modified brewer's yeast. We quantified evolutionary changes in growth rate, resource use efficiency (RUE), and their plasticity in strains evolving alone, with a competitor, and with a mutualist. Compared to their ancestors, strains evolving alone had lower RUE and RUE plasticity. There was also an evolutionary tradeoff between changes in growth rate and RUE in strains evolving alone, suggesting selection for increased growth rate at the cost of efficiency. Strains evolving with a competitive partner had higher growth rates, slightly lower RUE, and a stronger tradeoff between growth rate and efficiency. In contrast, mutualism had opposite effects on trait evolution. Strains evolving with a mutualist had slightly lower growth rates, higher RUE, and a weak evolutionary tradeoff between growth rate and RUE. Despite their different effects on trait evolution, competition and mutualism had little effect on plasticity evolution for either trait, suggesting that abiotic factors could be more important than biotic factors in generating selection for plasticity.

Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture

As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.

The Evolution of Gene Expression Plasticity During Adaptation to Salt in Chlamydomonas reinhardtii

When environmental change is rapid or unpredictable, phenotypic plasticity can facilitate adaptation to new or stressful environments to promote population persistence long enough for adaptive evolution to occur. However, the underlying genetic mechanisms that contribute to plasticity and its role in adaptive evolution are generally unknown. Two main opposing hypotheses dominate-genetic compensation and genetic assimilation. Here, we predominantly find evidence for genetic compensation over assimilation in adapting the freshwater algae Chlamydomonas reinhardtii to 36 g/L salt environments over 500 generations. More canalized genes in the high-salt (HS) lines displayed a pattern of genetic compensation (63%) fixing near or at the ancestral native expression level, rather than genetic assimilation of the salt-induced level, suggesting that compensation was more common during adaptation to salt. Network analysis revealed an enrichment of genes involved in energy production and salt-resistance processes in HS lines, while an increase in DNA repair mechanisms was seen in ancestral strains. In addition, whole-transcriptome similarity among ancestral and HS lines displayed the evolution of a similar plastic response to salt conditions in independently reared HS lines. We also found more cis-acting regions in the HS lines; however, the expression patterns of most genes did not mimic that of their inherited sequence. Thus, the expression changes induced via plasticity offer temporary relief, but downstream changes are required for a sustainable solution during the evolutionary process.

Strain-specific metabarcoding reveals rapid evolution of copper tolerance in populations of the coastal diatom Skeletonema marinoi

Phytoplankton have short generation times, flexible reproduction strategies, large population sizes and high standing genetic diversity, traits that should facilitate rapid evolution under directional selection. We quantified local adaptation of copper tolerance in a population of the diatom Skeletonema marinoi from a mining-exposed inlet in the Baltic Sea and in a non-exposed population 100 km away. We hypothesized that mining pollution has driven evolution of elevated copper tolerance in the impacted population of S. marinoi. Assays of 58 strains originating from sediment resting stages revealed no difference in the average tolerance to copper between the two populations. However, variation within populations was greater at the mining site, with three strains displaying hyper-tolerant phenotypes. In an artificial evolution experiment, we used a novel intraspecific metabarcoding locus to track selection and quantify fitness of all 58 strains during co-cultivation in one control and one toxic copper treatment. As expected, the hyper-tolerant strains enabled rapid evolution of copper tolerance in the mining-exposed population through selection on available strain diversity. Within 42 days, in each experimental replicate a single strain dominated (30%-99% abundance) but different strains dominated the different treatments. The reference population developed tolerance beyond expectations primarily due to slowly developing plastic response in one strain, suggesting that different modes of copper tolerance are present in the two populations. Our findings provide novel empirical evidence that standing genetic diversity of phytoplankton resting stage allows populations to evolve rapidly (20-50 generations) and flexibly on timescales relevant for seasonal bloom progressions.

Misalignment of plastic and evolutionary responses of lifespan to novel carbohydrate diets

Diet elicits varied effects on longevity across a wide range of animal species where dietary discordance between an organisms' evolutionary and developmental dietary history is increasingly recognized to play a critical role in shaping lifespan. However, whether such changes, predominantly assessed in a single generation, lead to evolutionary shifts in lifespan remains unclear. In this study, we used an experimental evolution approach to test whether changes in an organisms' evolutionary and developmental dietary history, specifically carbohydrate content, causes lifespan evolution in Drosophila serrata. After 30 generations, we investigated the evolutionary potential of lifespan in response to four novel diets that varied systematically in their ratio of carbohydrate-protein content. We also examined developmental plasticity effects using a set of control populations that were raised on the four novel environments allowing us to assess the extent to which plastic responses of lifespan mirrored adaptive responses observed following experimental evolution. Both high- and low-carbohydrate diets elicited plastic effects on lifespan; however, the plastic responses for lifespan to developmental diets bore little resemblance to the evolved responses on evolutionary diets. Understanding the dietary conditions regulating the match/mismatch of plastic and evolved responses will be important in determining whether a particular match/mismatch combination is adaptive for lifespan. While the differences in evolutionary diet by developmental diet interactions are only beginning to be elucidated, this study lays the foundation for future investigations of carbohydrate contributions to evolved and plastic effects on health and lifespan.

Resilience of Emiliania huxleyi to future changes in subantarctic waters

Lower pH and elevated temperature alter phytoplankton growth and biomass in short-term incubations, but longer-term responses and adaptation potential are less well-studied. To determine the future of the coccolithophore Emiliania huxleyi, a mixed genotype culture from subantarctic water was incubated for 720 days under present-day temperature and pH, and also projected future conditions by the year 2100. The future population exhibited a higher growth rate relative to present-day cells transferred to future conditions after 309 days, indicating adaptation or genotype selection; this was reflected by an increase in optimum growth temperature of ~2.5°C by the end of the experiment. Following transfer to opposing conditions in short-term cross-over incubations, cell volume responded rapidly, within eight generations, confirming trait plasticity. The changes in growth rate and cell volume were larger than reported in previous single stressor relationships and incubations, suggesting synergistic or additive effects of combined elevated temperature and lower pH and highlighting the importance of long-term multiple stressor experiments. At the end of the incubation there were no significant differences in cellular composition (particulate organic content and chlorophyll a), or primary production between present-day and future populations. Conversely, two independent methods showed a 50% decrease in both particulate inorganic carbon and calcification rate, consistent with the decrease in cell volume, in the future population. The observed plasticity and adaptive capacity of E. huxleyi indicate resilience to future conditions in subantarctic waters, although changes in cell volume and carbonate may alter grazing loss and cell ballast, so influencing carbon export to the deep ocean.

Local adaptation through countergradient selection in northern populations of Skeletonema marinoi

Marine microorganisms have the potential to disperse widely with few obvious barriers to gene flow. However, among microalgae, several studies have demonstrated that species can be highly genetically structured with limited gene flow among populations, despite hydrographic connectivity. Ecological differentiation and local adaptation have been suggested as drivers of such population structure. Here we tested whether multiple strains from two genetically distinct Baltic Sea populations of the diatom Skeletonema marinoi showed evidence of local adaptation to their local environments: the estuarine Bothnian Sea and the marine Kattegat Sea. We performed reciprocal transplants of multiple strains between culture media based on water from the respective environments, and we also allowed competition between strains of estuarine and marine origin in both salinities. When grown alone, both marine and estuarine strains performed best in the high-salinity environment, and estuarine strains always grew faster than marine strains. This result suggests local adaptation through countergradient selection, that is, genetic effects counteract environmental effects. However, the higher growth rate of the estuarine strains appears to have a cost in the marine environment and when strains were allowed to compete, marine strains performed better than estuarine strains in the marine environment. Thus, other traits are likely to also affect fitness. We provide evidence that tolerance to pH could be involved and that estuarine strains that are adapted to a more fluctuating pH continue growing at higher pH than marine strains.

Evidence for evolutionary adaptation of mixotrophic nanoflagellates to warmer temperatures

Mixotrophs, organisms that combine photosynthesis and heterotrophy to gain energy, play an important role in global biogeochemical cycles. Metabolic theory predicts that mixotrophs will become more heterotrophic with rising temperatures, potentially creating a positive feedback loop that accelerates carbon dioxide accumulation in the atmosphere. Studies testing this theory have focused on phenotypically plastic (short-term, non-evolutionary) thermal responses of mixotrophs. However, as small organisms with short generation times and large population sizes, mixotrophs may rapidly evolve in response to climate change. Here, we present data from a 3-year experiment quantifying the evolutionary response of two mixotrophic nanoflagellates to temperature. We found evidence for adaptive evolution (increased growth rates in evolved relative to acclimated lineages) in the obligately phototrophic strain, but not in the facultative phototroph. All lineages showed trends of increased carbon use efficiency, flattening of thermal reaction norms, and a return to homeostatic gene expression. Generally, mixotrophs evolved reduced photosynthesis and higher grazing with increased temperatures, suggesting that evolution may act to exacerbate mixotrophs' effects on global carbon cycling.

Trait drift in microalgae and applications for strain improvement

Microalgae are increasingly used to generate a wide range of commercial products, and there is growing evidence that microalgae-based products can be produced sustainably. However, industrial production of microalgal biomass is not as developed as other biomanufacturing platform technologies. In addition, results of bench-scale research often fail to translate to large-scale or mass production systems. This disconnect may result from trait drift and evolution occurring, through time, in response to unique drivers in each environment, such as cultivation regimes, weather, and pests. Moreover, outdoor and indoor cultivation of microalgae has the potential to impose negative selection pressures, which makes the maintenance of desired traits a challenge. In this context, this review sheds the light on our current understanding of trait drift and evolution in microalgae. We delineate the basics of phenotype plasticity and evolution, with a focus on how microalgae respond under various conditions. In addition, we review techniques that exploit phenotypic plasticity and evolution for strain improvement in view of industrial commercial applications, highlighting associated advantages and shortcomings. Finally, we suggest future research directions and recommendations to overcome unwanted trait drift and evolution in microalgae cultivation.

High Ecophysiological Plasticity of Desmarestia aculeata (Phaeophyceae) Present in an Arctic Fjord under Varying Salinity and Irradiance Conditions

The seaweed Desmarestia aculeata (Phaeophyceae) is distributed in the temperate zone of the North Atlantic up to the Arctic, where it is exposed to a high Arctic light regime and fluctuating salinity conditions resulting from glacial and terrestrial run-off. Information on how this species is able to thrive under current and future Arctic conditions is scarce. During the Arctic summer of 2019, D. aculeata was collected in Kongsfjorden, Svalbard (78.9° N, 11.9° E) to investigate its physiological and biochemical responses to variations in salinity (salinities: 34, 28 and 18) and daily cycles of irradiance (50-500 μmol photons m^-2s^-1) at 0 °C over 21 days. The species revealed effective short-term acclimation to both abiotic drivers. Maximal quantum yield of PSII (F_v/F_m) fluctuated with the light cycle at a salinity of 34, while the maximum relative electron transport rate (rETRmax) significantly differed between salinities of 28 and 18. Chlorophyll a and β-Carotene remained at high concentrations in all treatments showing pronounced acclimation during the experiment. High mannitol concentrations were measured throughout the experiment, while phlorotannins were high at low salinity. Hyposalinity and light are interacting drivers of the physiological and biochemical acclimation process for D. aculeata. Our experiment highlights the high ecophysiological plasticity of D. aculeata, suggesting that the species will likely be capable of withstanding future habitat changes in the Arctic.

Marine viruses and climate change: Virioplankton, the carbon cycle, and our future ocean

Interactions between marine viruses and microbes are a critical part of the oceanic carbon cycle. The impacts of virus-host interactions range from short-term disruptions in the mobility of microbial biomass carbon to higher trophic levels through cell lysis (i.e., the viral shunt) to long-term reallocation of microbial biomass carbon to the deep sea through accelerating the biological pump (i.e., the viral shuttle). The biogeochemical backdrop of the ocean-the physical, chemical, and biological landscape-influences the likelihood of both virus-host interactions and particle formation, and the fate and flow of carbon. As climate change reshapes the oceanic landscape through large-scale shifts in temperature, circulation, stratification, and acidification, virus-mediated carbon flux is likely to shift in response. Dynamics in the directionality and magnitude of changes in how, where, and when viruses mediate the recycling or storage of microbial biomass carbon is largely unknown. Integrating viral infection dynamics data obtained from experimental models and field systems, with particle motion microphysics and global observations of oceanic biogeochemistry, into improved ecosystem models will enable viral oceanographers to better predict the role of viruses in marine carbon cycling in the future ocean.

Marine Autotroph-Herbivore Synergies: Unravelling the Roles of Macroalgae in Marine Ecosystem Dynamics

Simple Summary

Invasive species are a leading hazard to marine ecosystems worldwide, coupled with climate change. Tackling the emerging biodiversity threat to maintain the ecological balance of the largest biome in the world has now become a pivotal part of the Sustainable Development Goals (SDGs). Marine herbivores are generally regarded as biological agents that restrict invasive species, and their efficiency depends on their dietary habits, especially the autotrophs they eat. Many researchers have found contradicting findings on the effects of nutritional attributes and novelty of autotrophs on herbivore eating behaviour. In light of the scattered literature on the mechanistic basis of autotroph-herbivore interactions, we provide a comprehensive review to fill knowledge gaps about synergies based on macroalgae, an important group of photosynthetic organisms in the marine biome that interact strongly with generalist herbivores. We also analyse macroalgal defence measures against herbivores, underlining unique features and potential roles in maintaining marine ecosystems. The nutritional qualities, shape, and novelty of autotrophs can alter herbivore feeding behaviour. Future research should explore aspects that can alter marine autotroph-herbivore interactions to resolve inconsistent results of specific features and the uniqueness of the organisms involved.

Abstract

Species invasion is a leading threat to marine ecosystems worldwide, being deemed as one of the ultimate jeopardies for biodiversity along with climate change. Tackling the emerging biodiversity threat to maintain the ecological balance of the largest biome in the world has now become a pivotal part of the Sustainable Development Goals (SDGs). Marine herbivores are often considered as biological agents that control the spread of invasive species, and their effectiveness depends largely on factors that influence their feeding preferences, including the specific attributes of their food–the autotrophs. While the marine autotroph-herbivore interactions have been substantially discussed globally, many studies have reported contradictory findings on the effects of nutritional attributes and novelty of autotrophs on herbivore feeding behaviour. In view of the scattered literature on the mechanistic basis of autotroph-herbivore interactions, we generate a comprehensive review to furnish insights into critical knowledge gaps about the synergies based largely on the characteristics of macroalgae; an important group of photosynthetic organisms in the marine biome that interact strongly with generalist herbivores. We also discuss the key defence strategies of these macroalgae against the herbivores, highlighting their unique attributes and plausible roles in keeping the marine ecosystems intact. Overall, the feeding behaviour of herbivores can be affected by the nutritional attributes, morphology, and novelty of the autotrophs. We recommend that future research should carefully consider different factors that can potentially affect the dynamics of the marine autotroph-herbivore interactions to resolve the inconsistent results of specific attributes and novelty of the organisms involved.

Evolution of thermal tolerance and phenotypic plasticity under rapid and slow temperature fluctuations

Global warming is associated with an increase in sea surface temperature and its variability. The consequences of evolving in variable, fluctuating environments are explored by a large body of theory: when populations evolve in fluctuating environments the frequency of fluctuations determines the shapes of tolerance curves (indicative of habitats that organisms can inhabit) and trait reaction norms (the phenotypes that organisms display across these environments). Despite this well-established theoretical backbone, predicting how trait and tolerance curves will evolve in organisms at the foundation of marine ecosystems remains a challenge. Here, we used a globally distributed phytoplankton, Thalassiosira pseudonana, and show that fluctuations in temperature on scales of 3–4 generations rapidly selected for populations with enhanced trait plasticity and elevated thermal tolerance. Fluctuations spanning 30–40 generations selected for the formation of two stable, genetically and physiologically distinct populations, one evolving high trait plasticity and enhanced thermal tolerance, and the other, akin to samples evolved under constant warming, with lower trait plasticity and a smaller increase in thermal tolerance.

Metabolic Adaptation of a Globally Important Diatom following 700 Generations of Selection under a Warmer Temperature

Diatoms, accounting for 40% of the marine primary production and 20% of global carbon dioxide fixation, are threatened by the ongoing ocean warming (OW). However, whether and how these ecologically important phytoplankton adapt to OW remains poorly unknown. Here, we experimentally examined the metabolic adaptation of a globally important diatom species Skeletonema dohrnii (S. dohrnii) to OW at two elevated temperatures (24 and 28 °C compared with 20 °C) under short-term (∼300 generations) and long-term (∼700 generations) selection. Both warming levels significantly increased the cell growth rate but decreased the chlorophyll a content. The contents of particulate organic carbon (POC) and particulate organic nitrogen (PON) decreased significantly initially (i.e., until 300 generations) at two temperature treatments but completely recovered after 700 generations of selection, suggesting that S. dohrnii ultimately developed thermal adaptation. Proteomic analysis demonstrated that elevated temperatures upregulated energy metabolism via glycolysis, tricarboxylic acid cycle, and fatty acid oxidation as well as nitrogen acquisition and utilization, which in turn reduced substance storage because of trade-off in the 300th generation, thus decreasing POC and PON. Interestingly, populations at both elevated temperatures exhibited significant proteome plasticity in the 700th generation, as primarily demonstrated by the increased lipid catabolism and glucose accumulation, accounting for the recovery of POC and PON. Changes occurring in cells at the 300th and 700th generations demonstrate that S. dohrnii can adapt to the projected OW, and readjusting the energy metabolism is an important adaptive strategy.

Loss of transcriptional plasticity but sustained adaptive capacity after adaptation to global change conditions in a marine copepod

Adaptive evolution and phenotypic plasticity will fuel resilience in the geologically unprecedented warming and acidification of the earth’s oceans, however, we have much to learn about the interactions and costs of these mechanisms of resilience. Here, using 20 generations of experimental evolution followed by three generations of reciprocal transplants, we investigated the relationship between adaptation and plasticity in the marine copepod, Acartia tonsa, in future global change conditions (high temperature and high CO₂). We found parallel adaptation to global change conditions in genes related to stress response, gene expression regulation, actin regulation, developmental processes, and energy production. However, reciprocal transplantation showed that adaptation resulted in a loss of transcriptional plasticity, reduced fecundity, and reduced population growth when global change-adapted animals were returned to ambient conditions or reared in low food conditions. However, after three successive transplant generations, global change-adapted animals were able to match the ambient-adaptive transcriptional profile. Concurrent changes in allele frequencies and erosion of nucleotide diversity suggest that this recovery occurred via adaptation back to ancestral conditions. These results demonstrate that while plasticity facilitated initial survival in global change conditions, it eroded after 20 generations as populations adapted, limiting resilience to new stressors and previously benign environments.

Rapid adaptation will facilitate species resilience under global climate change, but its effects on plasticity are less commonly investigated. This study shows that 20 generations of experimental adaptation in a marine copepod drives a rapid loss of plasticity that carries costs and might have impacts on future resilience to environmental change.

A reduction in metabolism explains the tradeoffs associated with the long-term adaptation of phytoplankton to high CO2 concentrations

Phytoplankton are responsible for nearly half of global primary productivity and play crucial roles in the Earth's biogeochemical cycles. However, the long-term adaptive responses of phytoplankton to rising CO₂ remains unknown. Here we examine the physiological and proteomics responses of a marine diatom, Phaeodactylum tricornutum, following long-term (c. 900 generations) selection to high CO₂ conditions. Our results show that this diatom responds to long-term high CO₂ selection by downregulating proteins involved in energy production (Calvin cycle, tricarboxylic acid cycle, glycolysis, oxidative pentose phosphate pathway), with a subsequent decrease in photosynthesis and respiration. Nearly similar extents of downregulation of photosynthesis and respiration allow the high CO₂ -adapted populations to allocate the same fraction of carbon to growth, thereby maintaining their fitness during the long-term high CO₂ selection. These results indicate an important role of metabolism reduction under high CO₂ and shed new light on the adaptive mechanisms of phytoplankton in response to climate change.

Biogeographic Population Structure of Chimeric Blades of Porphyra in the Northeast Atlantic Reveals Southern Rich Gene Pools, Introgression and Cryptic Plasticity

The genus Porphyra sensu lato (Bangiaceae, Rhodophyta), an important seaweed grown in aquaculture, is the most genetically diverse group of the Class Bangiophyceae, but has poorly understood genetic variability linked to complex evolutionary processes. Genetic studies in the last decades have largely focused on resolving gene phylogenies; however, there is little information on historical population biogeography, structure and gene flow in the Bangiaceae, probably due to their cryptic nature, chimerism and polyploidy, which render analyses challenging. This study aims to understand biogeographic population structure in the two abundant Porphyra species in the Northeast Atlantic: Porphyra dioica (a dioecious annual) and Porphyra linearis (protandrous hermaphroditic winter annual), occupying distinct niches (seasonality and position on the shore). Here, we present a large-scale biogeographic genetic analysis across their distribution in the Northeast Atlantic, using 10 microsatellites and cpDNA as genetic markers and integrating chimerism and polyploidy, including simulations considering alleles derived from different ploidy levels and/or from different genotypes within the chimeric blade. For P. linearis, both markers revealed strong genetic differentiation of north-central eastern Atlantic populations (from Iceland to the Basque region of Northeast Iberia) vs. southern populations (Galicia in Northwest Iberia, and Portugal), with higher genetic diversity in the south vs. a northern homogenous low diversity. For. P. dioica, microsatellite analyses also revealed two genetic regions, but with weaker differentiation, and cpDNA revealed little structure with all the haplotypes mixed across its distribution. The southern cluster in P. linearis also included introgressed individuals with cpDNA from P. dioica and a winter form of P. dioica occurred spatially intermixed with P. linearis. This third entity had a similar morphology and seasonality as P. linearis but genomes (either nuclear or chloroplast) from P. dioica. We hypothesize a northward colonization from southern Europe (where the ancestral populations reside and host most of the gene pool of these species). In P. linearis recently established populations colonized the north resulting in homogeneous low diversity, whereas for P. dioica the signature of this colonization is not as obvious due to hypothetical higher gene flow among populations, possibly linked to its reproductive biology and annual life history.

Spatial variation in high temperature-regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower

A major way that organisms can adapt to changing environmental conditions is by evolving increased or decreased phenotypic plasticity. In the face of current global warming, more attention is being paid to the role of plasticity in maintaining fitness as abiotic conditions change over time. However, given that temporal data can be challenging to acquire, a major question is whether evolution in plasticity across space can predict adaptive plasticity across time. In growth chambers simulating two thermal regimes, we generated transcriptome data for western North American scarlet monkeyflowers (Mimulus cardinalis) collected from different latitudes and years (2010 and 2017) to test hypotheses about how plasticity in gene expression is responding to increases in temperature, and if this pattern is consistent across time and space. Supporting the genetic compensation hypothesis, individuals whose progenitors were collected from the warmer-origin northern 2017 descendant cohort showed lower thermal plasticity in gene expression than their cooler-origin northern 2010 ancestors. This was largely due to a change in response at the warmer (40°C) rather than cooler (20°C) treatment. A similar pattern of reduced plasticity, largely due to a change in response at 40°C, was also found for the cooler-origin northern versus the warmer-origin southern population from 2017. Our results demonstrate that reduced phenotypic plasticity can evolve with warming and that spatial and temporal changes in plasticity predict one another.

Physiological Consequences of Oceanic Environmental Variation: Life from a Pelagic Organism's Perspective

To better understand life in the sea, marine scientists must first quantify how individual organisms experience their environment, and then describe how organismal performance depends on that experience. In this review, we first explore marine environmental variation from the perspective of pelagic organisms, the most abundant life forms in the ocean. Generation time, the ability to move relative to the surrounding water (even slowly), and the presence of environmental gradients at all spatial scales play dominant roles in determining the variation experienced by individuals, but this variation remains difficult to quantify. We then use this insight to critically examine current understanding of the environmental physiology of pelagic marine organisms. Physiologists have begun to grapple with the complexity presented by environmental variation, and promising frameworks exist for predicting and/or interpreting the consequences for physiological performance. However, new technology needs to be developed and much difficult empirical work remains, especially in quantifying response times to environmental variation and the interactions among multiple covarying factors. We call on the field of global-change biology to undertake these important challenges.

Evolution of Thermal Sensitivity in Changing and Variable Climates

Evolutionary adaptation to temperature and climate depends on both the extent to which organisms experience spatial and temporal environmental variation (exposure) and how responsive they are to the environmental variation (sensitivity). Theoretical models and experiments suggesting substantial potential for thermal adaptation have largely omitted realistic environmental variation. Environmental variation can drive fluctuations in selection that slow adaptive evolution. We review how carefully filtering environmental conditions based on how organisms experience their environment and further considering organismal sensitivity can improve predictions of thermal adaptation. We contrast taxa differing in exposure and sensitivity. Plasticity can increase the rate of evolutionary adaptation in taxa exposed to pronounced environmental variation. However, forms of plasticity that severely limit exposure, such as behavioral thermoregulation and phenological shifts, can hinder thermal adaptation. Despite examples of rapid thermal adaptation, experimental studies often reveal evolutionary constraints. Further investigating these constraints and issues of timescale and thermal history are needed to predict evolutionary adaptation and, consequently, population persistence in changing and variable environments.

Adaptive Phenotypic Plasticity Stabilizes Evolution in Fluctuating Environments

Fluctuating environmental conditions are ubiquitous in natural systems, and populations have evolved various strategies to cope with such fluctuations. The particular mechanisms that evolve profoundly influence subsequent evolutionary dynamics. One such mechanism is phenotypic plasticity, which is the ability of a single genotype to produce alternate phenotypes in an environmentally dependent context. Here, we use digital organisms (self-replicating computer programs) to investigate how adaptive phenotypic plasticity alters evolutionary dynamics and influences evolutionary outcomes in cyclically changing environments. Specifically, we examined the evolutionary histories of both plastic populations and non-plastic populations to ask: (1) Does adaptive plasticity promote or constrain evolutionary change? (2) Are plastic populations better able to evolve and then maintain novel traits? And (3), how does adaptive plasticity affect the potential for maladaptive alleles to accumulate in evolving genomes? We find that populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, which must rely on genetic variation from de novo mutations to continuously readapt to environmental fluctuations. Indeed, the non-plastic populations undergo more frequent selective sweeps and accumulate many more genetic changes. We find that the repeated selective sweeps in non-plastic populations drive the loss of beneficial traits and accumulation of maladaptive alleles, whereas phenotypic plasticity can stabilize populations against environmental fluctuations. This stabilization allows plastic populations to more easily retain novel adaptive traits than their non-plastic counterparts. In general, the evolution of adaptive phenotypic plasticity shifted evolutionary dynamics to be more similar to that of populations evolving in a static environment than to non-plastic populations evolving in an identical fluctuating environment. All natural environments subject populations to some form of change; our findings suggest that the stabilizing effect of phenotypic plasticity plays an important role in subsequent adaptive evolution.

Fluctuating selection and global change: a synthesis and review on disentangling the roles of climate amplitude, predictability and novelty

A formidable challenge for global change biologists is to predict how natural populations will respond to the emergence of conditions not observed at present, termed novel climates. Popular approaches to predict population vulnerability are based on the expected degree of novelty relative to the amplitude of historical climate fluctuations experienced by a population. Here, we argue that predictions focused on amplitude may be inaccurate because they ignore the predictability of environmental fluctuations in driving patterns of evolution and responses to climate change. To address this disconnect, we review major findings of evolutionary theory demonstrating the conditions under which phenotypic plasticity is likely to evolve in natural populations, and how plasticity decreases population vulnerability to novel environments. We outline key criteria that experimental studies should aim for to effectively test theoretical predictions, while controlling for the degree of climate novelty. We show that such targeted tests of evolutionary theory are rare, with marine systems being overall underrepresented in this venture despite exhibiting unique opportunities to test theory. We conclude that with more robust experimental designs that manipulate both the amplitude and predictability of fluctuations, while controlling for the degree of novelty, we may better predict population vulnerability to climate change.

Selection Experiments in the Sea: What Can Experimental Evolution Tell Us About How Marine Life Will Respond to Climate Change?

AbstractRapid evolution may provide a buffer against extinction risk for some species threatened by climate change; however, the capacity to evolve rapidly enough to keep pace with changing environments is unknown for most taxa. The ecosystem-level consequences of climate adaptation are likely to be the largest in marine ecosystems, where short-lived phytoplankton with large effective population sizes make up the bulk of primary production. However, there are substantial challenges to predicting climate-driven evolution in marine systems, including multiple simultaneous axes of change and considerable heterogeneity in rates of change, as well as the biphasic life cycles of many marine metazoans, which expose different life stages to disparate sources of selection. A critical tool for addressing these challenges is experimental evolution, where populations of organisms are directly exposed to controlled sources of selection to test evolutionary responses. We review the use of experimental evolution to test the capacity to adapt to climate change stressors in marine species. The application of experimental evolution in this context has grown dramatically in the past decade, shedding light on the capacity for evolution, associated trade-offs, and the genetic architecture of stress-tolerance traits. Our goal is to highlight the utility of this approach for investigating potential responses to climate change and point a way forward for future studies.

Growth strategies of a model picoplankter depend on social milieu and pCO2

Phytoplankton exist in genetically diverse populations, but are often studied as single lineages (single strains), so that interpreting single-lineage studies relies critically on understanding how microbial growth differs with social milieu, defined as the presence or absence of conspecifics. The properties of lineages grown alone often fail to predict the growth of these same lineages in the presence of conspecifics, and this discrepancy points towards an opportunity to improve our understanding of the factors that affect lineage growth rates. We demonstrate that different lineages of a marine picoplankter modulate their maximum lineage growth rate in response to the presence of non-self conspecifics, even when resource competition is effectively absent. This explains why growth rates of lineages in isolation do not reliably predict their growth rates in mixed culture, or the lineage composition of assemblages under conditions of rapid growth. The diversity of growth strategies observed here are consistent with lineage-specific energy allocation that depends on social milieu. Since lineage growth is only one of many traits determining fitness in natural assemblages, we hypothesize that intraspecific variation in growth strategies should be common, with more strategies possible in ameliorated environments that support higher maximum growth rates, such as high CO2 for many marine picoplankton.

Acclimation and adaptation to elevated pCO2 increase arsenic resilience in marine diatoms

Arsenic pollution is a widespread threat to marine life, but the ongoing rise pCO₂ levels is predicted to decrease bio-toxicity of arsenic. However, the effects of arsenic toxicity on marine primary producers under elevated pCO₂ are not well characterized. Here, we studied the effects of arsenic toxicity in three globally distributed diatom species (Phaeodactylum tricornutum, Thalassiosira pseudonana, and Chaetoceros mulleri) after short-term acclimation (ST, 30 days), medium-term exposure (MT, 750 days), and long-term (LT, 1460 days) selection under ambient (400 µatm) and elevated (1000 and 2000 µatm) pCO₂. We found that elevated pCO₂ alleviated arsenic toxicity even after short acclimation times but the magnitude of the response decreased after mid and long-term adaptation. When fed with these elevated pCO₂ selected diatoms, the scallop Patinopecten yessoensis had significantly lower arsenic content (3.26-52.83%). Transcriptomic and biochemical analysis indicated that the diatoms rapidly developed arsenic detoxification strategies, which included upregulation of transporters associated with shuttling harmful compounds out of the cell to reduce arsenic accumulation, and upregulation of proteins involved in synthesizing glutathione (GSH) to chelate intracellular arsenic to reduce arsenic toxicity. Thus, our results will expand our knowledge to fully understand the ecological risk of trace metal pollution under increasing human activity induced ocean acidification.

Rapid multi-generational acclimation of coralline algal reproductive structures to ocean acidification

The future of coral reef ecosystems is under threat because vital reef-accreting species such as coralline algae are highly susceptible to ocean acidification. Although ocean acidification is known to reduce coralline algal growth rates, its direct effects on the development of coralline algal reproductive structures (conceptacles) is largely unknown. Furthermore, the long-term, multi-generational response of coralline algae to ocean acidification is extremely understudied. Here, we investigate how mean pH, pH variability and the pH regime experienced in their natural habitat affect coralline algal conceptacle abundance and size across six generations of exposure. We show that second-generation coralline algae exposed to ocean acidification treatments had conceptacle abundances 60% lower than those kept in present-day conditions, suggesting that conceptacle development is initially highly sensitive to ocean acidification. However, this negative effect of ocean acidification on conceptacle abundance disappears after three generations of exposure. Moreover, we show that this transgenerational acclimation of conceptacle development is not facilitated by a trade-off with reduced investment in growth, as higher conceptacle abundances are associated with crusts with faster growth rates. These results indicate that the potential reproductive output of coralline algae may be sustained under future ocean acidification.

Adaptive responses of free-living and symbiotic microalgae to simulated future ocean conditions

Marine microalgae are a diverse group of microscopic eukaryotic and prokaryotic organisms capable of photosynthesis. They are important primary producers and carbon sinks but their physiology and persistence are severely affected by global climate change. Powerful experimental evolution technologies are being used to examine the potential of microalgae to respond adaptively to current and predicted future conditions, as well as to develop resources to facilitate species conservation and restoration of ecosystem functions. This review synthesizes findings and insights from experimental evolution studies of marine microalgae in response to elevated temperature and/or pCO₂ . Adaptation to these environmental conditions has been observed in many studies of marine dinoflagellates, diatoms and coccolithophores. An enhancement in traits such as growth and photo-physiological performance and an increase in upper thermal limit have been shown to be possible, although the extent and rate of change differ between microalgal taxa. Studies employing multiple monoclonal replicates showed variation in responses among replicates and revealed the stochasticity of mutations. The work to date is already providing valuable information on species' climate sensitivity or resilience to managers and policymakers but extrapolating these insights to ecosystem- and community-level impacts continues to be a challenge. We recommend future work should include in situ experiments, diurnal and seasonal fluctuations, multiple drivers and multiple starting genotypes. Fitness trade-offs, stable versus plastic responses and the genetic bases of the changes also need investigating, and the incorporation of genome resequencing into experimental designs will be invaluable.

Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium

A major challenge in modern biology is understanding how the effects of short-term biological responses influence long-term evolutionary adaptation, defined as a genetically determined increase in fitness to novel environments. This is particularly important in globally important microbes experiencing rapid global change, due to their influence on food webs, biogeochemical cycles, and climate. Epigenetic modifications like methylation have been demonstrated to influence short-term plastic responses, which ultimately impact long-term adaptive responses to environmental change. However, there remains a paucity of empirical research examining long-term methylation dynamics during environmental adaptation in nonmodel, ecologically important microbes. Here, we show the first empirical evidence in a marine prokaryote for long-term m5C methylome modifications correlated with phenotypic adaptation to CO2, using a 7-year evolution experiment (1,000+ generations) with the biogeochemically important marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly changed in response to high (750 µatm) CO2 exposure and were maintained for at least 4.5 years of CO2 selection. After 7 years of CO2 selection, however, m5C methylation levels that initially responded to high-CO2 returned to ancestral, ambient CO2 levels. Concurrently, high-CO2 adapted growth and N2 fixation rates remained significantly higher than those of ambient CO2 adapted cell lines irrespective of CO2 concentration, a trend consistent with genetic assimilation theory. These data demonstrate the maintenance of CO2-responsive m5C methylation for 4.5 years alongside phenotypic adaptation before returning to ancestral methylation levels. These observations in a globally distributed marine prokaryote provide critical evolutionary insights into biogeochemically important traits under global change.

The role of changes in environmental quality in multitrait plastic responses to environmental and social change in the model microalga Chlamydomonas reinhardtii

Intraspecific variation plays a key role in species' responses to environmental change; however, little is known about the role of changes in environmental quality (the population growth rate an environment supports) on intraspecific trait variation. Here, we hypothesize that intraspecific trait variation will be higher in ameliorated environments than in degraded ones. We first measure the range of multitrait phenotypes over a range of environmental qualities for three strains and two evolutionary histories of Chlamydomonas reinhardtii in laboratory conditions. We then explore how environmental quality and trait variation affect the predictability of lineage frequencies when lineage pairs are grown in indirect co-culture. Our results show that environmental quality has the potential to affect intraspecific variability both in terms of the variation in expressed trait values, and in terms of the genotype composition of rapidly growing populations. We found low phenotypic variability in degraded or same-quality environments and high phenotypic variability in ameliorated conditions. This variation can affect population composition, as monoculture growth rate is a less reliable predictor of lineage frequencies in ameliorated environments. Our study highlights that understanding whether populations experience environmental change as an increase or a decrease in quality relative to their recent history affects the changes in trait variation during plastic responses, including growth responses to the presence of conspecifics. This points toward a fundamental role for changes in overall environmental quality in driving phenotypic variation within closely related populations, with implications for microevolution.

Temperature fluctuations in a warmer environment: impacts on microbial plankton

Warming can cause changes in the structure and functioning of microbial food webs. Experimental studies quantifying such impacts on microbial plankton have tended to consider constant temperature conditions. However, Jensen's inequality (or the fallacy of the average) recognizes that organism performance under constant conditions is seldom equal to the mean performance under variable conditions, highlighting the need to consider in situ fluctuations over a range of time scales. Here we review some of the available evidence on how warming effects on the abundance, diversity, and metabolism of microbial plankton are altered when temperature fluctuations are considered. We found that fluctuating temperatures may accentuate warming-mediated reductions in phytoplankton evenness and gross photosynthesis while synergistically increasing phytoplankton growth. Also, fluctuating temperatures have been shown to reduce the positive warming effect on cyanobacterial biomass production and recruitment and to reverse a warming effect on cellular nutrient quotas. Other reports have shown that fluctuations in temperature did not alter plankton responses to constant warming. These investigations have mostly focused on a few phytoplankton species (i.e. diatoms and haptophytes) in temperate and marine ecosystems and considered short-term and transient responses. It remains unknown whether the same responses apply to other species and ecosystems and if evolutionary change in thermally varying environments could alter the magnitude and direction of the responses to warming observed over short-term scales. Thus, future research efforts should address the role of fluctuations in environmental drivers. We stress the need to study responses over different biological organization and trophic levels, nutritional modes, temporal scales, and ecosystem types.

Ancestral genetic variation in phenotypic plasticity underlies rapid evolutionary changes in resurrected populations of waterfleas

The role of phenotypic plasticity in adaptive evolution has been debated for decades. This is because the strength of natural selection is dependent on the direction and magnitude of phenotypic responses to environmental signals. Therefore, the connection between plasticity and adaptation will depend on the patterns of plasticity harbored by ancestral populations before a change in the environment. Yet few studies have directly assessed ancestral variation in plasticity and tracked phenotypic changes over time. Here we resurrected historic propagules of Daphnia spanning multiple species and lakes in Wisconsin following the invasion and proliferation of a novel predator (spiny waterflea, Bythotrephes longimanus). This approach revealed extensive genetic variation in predator-induced plasticity in ancestral populations of Daphnia It is unlikely that the standing patterns of plasticity shielded Daphnia from selection to permit long-term coexistence with a novel predator. Instead, this variation in plasticity provided the raw materials for Bythotrephes-mediated selection to drive rapid shifts in Daphnia behavior and life history. Surprisingly, there was little evidence for the evolution of trait plasticity as genetic variation in plasticity was maintained in the face of a novel predator. Such results provide insight into the link between plasticity and adaptation and highlight the importance of quantifying genetic variation in plasticity when evaluating the drivers of evolutionary change in the wild.

Evolution of Generalists by Phenotypic Plasticity

Adapting organisms face a tension between specializing their phenotypes for certain ecological tasks and developing generalist strategies that permit persistence in multiple environmental conditions. Understanding when and how generalists or specialists evolve is an important question in evolutionary dynamics. Here, we study the evolution of bacterial range expansions by selecting Escherichia coli for faster migration through porous media containing one of four different sugars supporting growth and chemotaxis. We find that selection in any one sugar drives the evolution of faster migration in all sugars. Measurements of growth and motility of all evolved lineages in all nutrient conditions reveal that the ubiquitous evolution of fast migration arises via phenotypic plasticity. Phenotypic plasticity permits evolved strains to exploit distinct strategies to achieve fast migration in each environment, irrespective of the environment in which they were evolved. Therefore, selection in a homogeneous environment drives phenotypic plasticity that improves performance in other environments.

Functional redundancy in natural pico-phytoplankton communities depends on temperature and biogeography

Biodiversity affects ecosystem function, and how this relationship will change in a warming world is a major and well-examined question in ecology. Yet, it remains understudied for pico-phytoplankton communities, which contribute to carbon cycles and aquatic food webs year-round. Observational studies show a link between phytoplankton community diversity and ecosystem stability, but there is only scarce causal or empirical evidence. Here, we sampled phytoplankton communities from two geographically related regions with distinct thermal and biological properties in the Southern Baltic Sea and carried out a series of dilution/regrowth experiments across three assay temperatures. This allowed us to investigate the effects of loss of rare taxa and establish causal links in natural communities between species richness and several ecologically relevant traits (e.g. size, biomass production, and oxygen production), depending on sampling location and assay temperature. We found that the samples' biogeographical origin determined whether and how functional redundancy changed as a function of temperature for all traits under investigation. Samples obtained from the slightly warmer and more thermally variable regions showed overall high functional redundancy. Samples from the slightly cooler, less variable, stations showed little functional redundancy, i.e. function decreased when species were lost from the community. The differences between regions were more pronounced at elevated assay temperatures. Our results imply that the importance of rare species and the amount of species required to maintain ecosystem function even under short-term warming may differ drastically even within geographically closely related regions of the same ecosystem.

Different genetic basis for alcohol dehydrogenase activity and plasticity in a novel alcohol environment for Drosophila melanogaster

Phenotypic plasticity is known to enhance population persistence, facilitate adaptive evolution and initiate novel phenotypes in novel environments. How plasticity can contribute or hinder adaptation to different environments hinges on its genetic architecture. Even though plasticity in many traits is genetically controlled, whether and how plasticity's genetic architecture might change in novel environments is still unclear. Because much of gene expression can be environmentally influenced, each environment may trigger different sets of genes that influence a trait. Using a quantitative trait loci (QTL) approach, we investigated the genetic basis of plasticity in a classic functional trait, alcohol dehydrogenase (ADH) activity in D. melanogaster, across both historical and novel alcohol environments. Previous research in D. melanogaster has also demonstrated that ADH activity is plastic in response to alcohol concentration in substrates used by both adult flies and larvae. We found that across all environments tested, ADH activity was largely influenced by a single QTL encompassing the Adh-coding gene and its known regulatory locus, delta-1. After controlling for the allelic variation of the Adh and delta-1 loci, we found additional but different minor QTLs in the 0 and 14% alcohol environments. In contrast, we discovered no major QTL for plasticity itself, including the Adh locus, regardless of the environmental gradients. This suggests that plasticity in ADH activity is likely influenced by many loci with small effects, and that the Adh locus is not environmentally sensitive to dietary alcohol.

The lag-time constraint for behavioural plasticity

Environmental instability (i.e. environments changing often) can select fixed phenotypes because of the lag time of plastically adapting to environmental changes, known as the lag-time constraint. Because behaviour can change rapidly (e.g. switching between foraging strategies), the lag-time constraint is not considered important for behavioural plasticity. Instead, it is often argued that responsive behaviour (i.e. behaviour that changes according to the environment) evolves to cope with unstable environments. But proficiently performing certain behaviours may require time for learning, for practising or, in social animals, for the group to adjust to one's behaviour. Conversely, not using certain behaviours for a period of time can reduce their level of performance. Here, using individual-based evolutionary simulations, we show that environmental instability selects for fixed behaviour when the ratio between the rates of increase and reduction in behavioural performance is below a certain threshold; only above this threshold does responsive behaviour evolve in unstable environments. Thus, the lag-time constraint can apply to behaviours that attain high performance either slowly or rapidly, depending on the relative rate with which their performance decreases when not used. We discuss these results in the context of the evolution of reduced behavioural plasticity, as seen in fixed personality differences.

Multiple global change stressor effects on phytoplankton nutrient acquisition in a future ocean

Predicting the effects of multiple global change stressors on microbial communities remains a challenge because of the complex interactions among those factors. Here, we explore the combined effects of major global change stressors on nutrient acquisition traits in marine phytoplankton. Nutrient limitation constrains phytoplankton production in large parts of the present-day oceans, and is expected to increase owing to climate change, potentially favouring small phytoplankton that are better adapted to oligotrophic conditions. However, other stressors, such as elevated pCO2, rising temperatures and higher light levels, may reduce general metabolic and photosynthetic costs, allowing the reallocation of energy to the acquisition of increasingly limiting nutrients. We propose that this energy reallocation in response to major global change stressors may be more effective in large-celled phytoplankton species and, thus, could indirectly benefit large-more than small-celled phytoplankton, offsetting, at least partially, competitive disadvantages of large cells in a future ocean. Thus, considering the size-dependent responses to multiple stressors may provide a more nuanced understanding of how different microbial groups would fare in the future climate and what effects that would have on ecosystem functioning. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Gene regulation underpinning increased thermal tolerance in a laboratory-evolved coral photosymbiont

Small increases in ocean temperature can disrupt the obligate symbiosis between corals and dinoflagellate microalgae, resulting in coral bleaching. Little is known about the genes that drive the physiological and bleaching response of algal symbionts to elevated temperature. Moreover, many studies to-date have compared highly divergent strains, making it challenging to accredit specific genes to contrasting traits. Here, we compare transcriptional responses at ambient (27°C) and bleaching-relevant (31°C) temperatures in a monoclonal, wild-type (WT) strain of Symbiodiniaceae to those of a selected-strain (SS), derived from the same monoclonal culture and experimentally evolved to elevated temperature over 80 generations (2.5 years). Thousands of genes were differentially expressed at a log fold-change of >8 between the WT and SS over a 35 days temperature treatment period. At 31°C, WT cells exhibited a temporally unstable transcriptomic response upregulating genes involved in the universal stress response such as molecular chaperoning, protein repair, protein degradation and DNA repair. Comparatively, SS cells exhibited a temporally stable transcriptomic response and downregulated many stress response genes that were upregulated by the WT. Among the most highly upregulated genes in the SS at 31°C were algal transcription factors and a gene probably of bacterial origin that encodes a type II secretion system protein, suggesting interactions with bacteria may contribute to the increased thermal tolerance of the SS. Genes and functional pathways conferring thermal tolerance in the SS could be targeted in future genetic engineering experiments designed to develop thermally resilient algal symbionts for use in coral restoration and conservation.

Microbial evolutionary strategies in a dynamic ocean

Marine microbes form the base of ocean food webs and drive ocean biogeochemical cycling. Yet little is known about the ability of microbial populations to adapt as they are advected through changing conditions. Here, we investigated the interplay between physical and biological timescales using a model of adaptation and an eddy-resolving ocean circulation climate model. Two criteria were identified that relate the timing and nature of adaptation to the ratio of physical to biological timescales. Genetic adaptation was impeded in highly variable regimes by nongenetic modifications but was promoted in more stable environments. An evolutionary trade-off emerged where greater short-term nongenetic transgenerational effects (low-γ strategy) enabled rapid responses to environmental fluctuations but delayed genetic adaptation, while fewer short-term transgenerational effects (high-γ strategy) allowed faster genetic adaptation but inhibited short-term responses. Our results demonstrate that the selective pressures for organisms within a single water mass vary based on differences in generation timescales resulting in different evolutionary strategies being favored. Organisms that experience more variable environments should favor a low-γ strategy. Furthermore, faster cell division rates should be a key factor in genetic adaptation in a changing ocean. Understanding and quantifying the relationship between evolutionary and physical timescales is critical for robust predictions of future microbial dynamics.

Adaptation to climate change through genetic accommodation and assimilation of plastic phenotypes

Theory suggests that evolutionary changes in phenotypic plasticity could either hinder or facilitate evolutionary rescue in a changing climate. Nevertheless, the actual role of evolving plasticity in the responses of natural populations to climate change remains unresolved. Direct observations of evolutionary change in nature are rare, making it difficult to assess the relative contributions of changes in trait means versus changes in plasticity to climate change responses. To address this gap, this review explores several proxies that can be used to understand evolving plasticity in the context of climate change, including space for time substitutions, experimental evolution and tests for genomic divergence at environmentally responsive loci. Comparisons among populations indicate a prominent role for divergence in environmentally responsive traits in local adaptation to climatic gradients. Moreover, genomic comparisons among such populations have identified pervasive divergence in the regulatory regions of environmentally responsive loci. Taken together, these lines of evidence suggest that divergence in plasticity plays a prominent role in adaptation to climatic gradients over space, indicating that evolving plasticity is also likely to play a key role in adaptive responses to climate change through time. This suggests that genetic variation in plastic responses to the environment (G × E) might be an important predictor of species' vulnerabilities to climate-driven decline or extinction. This article is part of the theme issue 'The role of plasticity in phenotypic adaptation to rapid environmental change'.

Quality-quantity trade-offs drive functional trait evolution in a model microalgal 'climate change winner'

Phytoplankton are the unicellular photosynthetic microbes that form the base of aquatic ecosystems, and their responses to global change will impact everything from food web dynamics to global nutrient cycles. Some taxa respond to environmental change by increasing population growth rates in the short-term and are projected to increase in frequency over decades. To gain insight into how these projected 'climate change winners' evolve, we grew populations of microalgae in ameliorated environments for several hundred generations. Most populations evolved to allocate a smaller proportion of carbon to growth while increasing their ability to tolerate and metabolise reactive oxygen species (ROS). This trade-off drives the evolution of traits that underlie the ecological and biogeochemical roles of phytoplankton. This offers evolutionary and a metabolic frameworks for understanding trait evolution in projected 'climate change winners' and suggests that short-term population booms have the potential to be dampened or reversed when environmental amelioration persists.

Evolution, Microbes, and Changing Ocean Conditions

Experimental evolution and the associated theory are underutilized in marine microbial studies; the two fields have developed largely in isolation. Here, we review evolutionary tools for addressing four key areas of ocean global change biology: linking plastic and evolutionary trait changes, the contribution of environmental variability to determining trait values, the role of multiple environmental drivers in trait change, and the fate of populations near their tolerance limits. Wherever possible, we highlight which data from marine studies could use evolutionary approaches and where marine model systems can advance our understanding of evolution. Finally, we discuss the emerging field of marine microbial experimental evolution. We propose a framework linking changes in environmental quality (defined as the cumulative effect on population growth rate) with population traits affecting evolutionary potential, in order to understand which evolutionary processes are likely to be most important across a range of locations for different types of marine microbes.

Ecological change in dynamic environments: Accounting for temporal environmental variability in studies of ocean change biology

The environmental conditions in the ocean have long been considered relatively more stable through time compared to the conditions on land. Advances in sensing technologies, however, are increasingly revealing substantial fluctuations in abiotic factors over ecologically and evolutionarily relevant timescales in the ocean, leading to a growing recognition of the dynamism of the marine environment as well as new questions about how this dynamism may influence species' vulnerability to global environmental change. In some instances, the diurnal or seasonal variability in major environmental change drivers, such as temperature, pH and seawater carbonate chemistry, and dissolved oxygen, can exceed the changes expected with continued anthropogenic global change. While ocean global change biologists have begun to experimentally test how variability in environmental conditions mediates species' responses to changes in the mean, the extensive literature on species' adaptations to temporal variability in their environment and the implications of this variability for their evolutionary responses has not been well integrated into the field. Here, we review the physiological mechanisms underlying species' responses to changes in temperature, pCO₂ /pH (and other carbonate parameters), and dissolved oxygen, and discuss what is known about behavioral, plastic, and evolutionary strategies for dealing with variable environments. In addition, we discuss how exposure to variability may influence species' responses to changes in the mean conditions and highlight key research needs for ocean global change biology.

Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms

Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.

Thermal plasticity is independent of environmental history in an intertidal seaweed

Organisms inhabiting the intertidal zone have been used to study natural ecophysiological responses and adaptations to thermal stress because these organisms are routinely exposed to high-temperature conditions for hours at a time. While intertidal organisms may be inherently better at withstanding temperature stress due to regular exposure and acclimation, they could be more vulnerable to temperature stress, already living near the edge of their thermal limits. Strong gradients in thermal stress across the intertidal zone present an opportunity to test whether thermal tolerance is a plastic or canalized trait in intertidal organisms. Here, we studied the intertidal pool-dwelling calcified alga, Ellisolandia elongata, under near-future temperature regimes, and the dependence of its thermal acclimatization response on environmental history. Two timescales of environmental history were tested during this experiment. The intertidal pool of origin was representative of long-term environmental history over the alga's life (including settlement and development), while the pool it was transplanted into accounted for recent environmental history (acclimation over many months). Unexpectedly, neither long-term nor short-term environmental history, nor ambient conditions, affected photosynthetic rates in E. elongata. Individuals were plastic in their photosynthetic response to laboratory temperature treatments (mean 13.2°C, 15.7°C, and 17.7°C). Further, replicate ramets from the same individual were not always consistent in their photosynthetic performance from one experimental time point to another or between treatments and exhibited no clear trend in variability over experimental time. High variability in climate change responses between individuals may indicate the potential for resilience to future conditions and, thus, may play a compensatory role at the population or species level over time.

Sensitivities to global change drivers may correlate positively or negatively in a foundational marine macroalga

Ecological impact of global change is generated by multiple synchronous or asynchronous drivers which interact with each other and with intraspecific variability of sensitivities. In three near-natural experiments, we explored response correlations of full-sibling germling families of the seaweed Fucus vesiculosus towards four global change drivers: elevated CO2 (ocean acidification, OA), ocean warming (OW), combined OA and warming (OAW), nutrient enrichment and hypoxic upwelling. Among families, performance responses to OA and OW as well as to OAW and nutrient enrichment correlated positively whereas performance responses to OAW and hypoxia anti-correlated. This indicates (i) that families robust to one of the three drivers (OA, OW, nutrients) will also not suffer from the two other shifts, and vice versa and (ii) families benefitting from OAW will more easily succumb to hypoxia. Our results may imply that selection under either OA, OW or eutrophication would enhance performance under the other two drivers but simultaneously render the population more susceptible to hypoxia. We conclude that intraspecific response correlations have a high potential to boost or hinder adaptation to multifactorial global change scenarios.

Different Nutritional Histories Affect the Susceptibility of Algae to Grazing

We hypothesize that algae with different cell compositions are differently perceived by their predators and consequently subjected to selective grazing. Five populations of the diatom Phaeodactylum tricornutum that differed in organic and elemental composition, but were otherwise identical, were generated by acclimation to distinct growth regimes. The different populations were then mixed in pairs and subjected to predation by either the rotifer Brachionus plicatilis or the copepod Acartia tonsa. The presence of rotifers had no impact on the ratio between any two algal populations. The presence of copepods, however, affected the ratio between algae previously acclimated to a medium containing 1 mM NH₄⁺ and algae acclimated to 0.5 mM NO₃^- , and to either a lower irradiance or a higher CO₂ concentration. We discuss the possible reason for the influence of different nutritional histories on the vulnerability of algae to predators. The differential impact of grazers on the growth of algae with different nutritional histories may result from direct selective grazing (i.e., grazers can detect algae with the most palatable cell composition), alone or combined to an asymmetric utilization of the nutrients regenerated after predation by co-existing algal populations. Our results strongly suggest that the nutritional history of algae can influence the relationships between phytoplankton and grazers and hint at the possibility that algal cell composition is potentially subject to natural selection, because it influences the probability that algae survive predation.