Company matters: The presence of other genotypes alters traits and intraspecific selection in an Arctic diatom under climate change

Genome-wide sequencing reveals geographical variations in the thermal adaptation of an aquaculture species with frequent seedling introductions

Climate change and human activity are essential factors affecting marine biodiversity and aquaculture, and understanding the impacts of human activities on the genetic structure to increasing high temperatures is crucial for sustainable aquaculture and marine biodiversity conservation. As a commercially important bivalve, the Manila clam Ruditapes philippinarum is widely distributed along the coast of China, and it has been frequently introduced from Fujian Province, China, to other regions for aquaculture. In this study, we collected four populations of Manila clams from different areas to evaluate their thermal tolerance by measuring cardiac performance and genetic variations using whole-genome resequencing. The upper thermal limits of the clams showed high variations within and among populations. Different populations displayed divergent genetic compositions, and the admixed population was partly derived from the Zhangzhou population in Fujian Province, implying a complex genomic landscape under the influence of local genetic sources and human introductions. Multiple single nucleotide polymorphisms (SNPs) were associated with the cardiac functional traits, and some of these SNPs can affect the codon usage and the structural stability of the resulting protein. This study shed light on the importance of establishing long-term ecological and genetic monitoring programs at the local level to enhance resilience to future climate change.

Heatwave responses of Arctic phytoplankton communities are driven by combined impacts of warming and cooling

Marine heatwaves are increasing in frequency and intensity as climate change progresses, especially in the highly productive Arctic regions. Although their effects on primary producers will largely determine the impacts on ecosystem services, mechanistic understanding on phytoplankton responses to these extreme events is still very limited. We experimentally exposed Arctic phytoplankton assemblages to stable warming, as well as to repeated heatwaves, and measured temporally resolved productivity, physiology, and composition. Our results show that even extreme stable warming increases productivity, while the response to heatwaves depends on the specific scenario applied and is not predictable from stable warming responses. This appears to be largely due to the underestimated impact of the cool phase following a heatwave, which can be at least as important as the warm phase for the overall response. We show that physiological and compositional adjustments to both warm and cool phases drive overall phytoplankton productivity and need to be considered mechanistically to predict overall ecosystem impacts.

A story of resilience: Arctic diatom Chaetoceros gelidus exhibited high physiological plasticity to changing CO2 and light levels

Arctic phytoplankton are experiencing multifaceted stresses due to climate warming, ocean acidification, retreating sea ice, and associated changes in light availability, and that may have large ecological consequences. Multiple stressor studies on Arctic phytoplankton, particularly on the bloom-forming species, may help understand their fitness in response to future climate change, however, such studies are scarce. In the present study, a laboratory experiment was conducted on the bloom-forming Arctic diatom Chaetoceros gelidus (earlier C. socialis) under variable CO₂ (240 and 900 µatm) and light (50 and 100 µmol photons m^-2 s^-1) levels. The growth response was documented using the pre-acclimatized culture at 2°C in a closed batch system over 12 days until the dissolved inorganic nitrogen was depleted. Particulate organic carbon and nitrogen (POC and PON), pigments, cell density, and the maximum quantum yield of photosystem II (Fv/Fm) were measured on day 4 (D₄), 6 (D₆), 10 (D₁₀), and 12 (D₁₂). The overall growth response suggested that C. gelidus maintained a steady-state carboxylation rate with subsequent conversion to macromolecules as reflected in the per-cell POC contents under variable CO₂ and light levels. A substantial amount of POC buildup at the low CO₂ level (comparable to the high CO₂ treatment) indicated the possibility of existing carbon dioxide concentration mechanisms (CCMs) that needs further investigation. Pigment signatures revealed a high level of adaptability to variable irradiance in this species without any major CO₂ effect. PON contents per cell increased initially but decreased irrespective of CO₂ levels when nitrogen was limited (D₆ onward) possibly to recycle intracellular nitrogen resources resulting in enhanced C: N ratios. On D₁₂ the decreased dissolved organic nitrogen levels could be attributed to consumption under nitrogen starvation. Such physiological plasticity could make C. gelidus "ecologically resilient" in the future Arctic.

Thermal trait variation may buffer Southern Ocean phytoplankton from anthropogenic warming

Despite the potential of standing genetic variation to rescue communities and shape future adaptation to climate change, high levels of uncertainty are associated with intraspecific trait variation in marine phytoplankton. Recent model intercomparisons have pointed to an urgent need to reduce uncertainty in the projected responses of marine ecosystems to climate change, including Southern Ocean (SO) surface waters, which are among the most rapidly warming habitats on Earth. Because SO phytoplankton growth responses to warming sea surface temperature (SST) are poorly constrained, we developed a high-throughput growth assay to simultaneously examine inter- and intra-specific thermal trait variation in a group of 43 taxonomically diverse and biogeochemically important SO phytoplankton called diatoms. We found significant differential growth performance among species across thermal traits, including optimum and maximum tolerated growth temperatures. Within species, coefficients of variation ranged from 3% to 48% among strains for those same key thermal traits. Using SO SST projections for 2100, we predicted biogeographic ranges that differed by up to 97% between the least and most tolerant strains for each species, illustrating the role that strain-specific differences in temperature response can play in shaping predictions of future phytoplankton biogeography. Our findings revealed the presence and scale of thermal trait variation in SO phytoplankton and suggest these communities may already harbour the thermal trait diversity required to withstand projected 21st-century SST change in the SO even under severe climate forcing scenarios.

Phytoplankton growth and community shift over a short-term high-CO2 simulation experiment from the southwestern shelf of India, Eastern Arabian Sea (summer monsoon)

The southwestern shelf water of India (eastern Arabian Sea) experiences high seasonality. This area is one of the understudied regions in terms of phytoplankton response to the projected ocean acidification, particularly, during the summer monsoon when phytoplankton abundance is high. Here we present the results of a short-term simulated ocean acidification experiment (ambient CO₂ 424 µatm; high CO₂, 843, 1138 µatm) on the natural phytoplankton assemblages conducted onboard (R. V. Sindhu Sadhana) during the summer monsoon (Aug 2017). Among the dissolved inorganic nutrients, dissolved silicate (DSi) and nitrate + nitrite levels were quite low (< 2 µM). Phytoplankton biomass did not show any net enhancement after the incubation in any treatment. Both marker pigment analysis and microscopy revealed the dominance of diatoms in the phytoplankton community, and a significant restructuring was noticed over the experimental period. Divinyl chlorophylla (DVChla) containing picocyanobacteria and 19'-hexanoyloxyfucoxanthin (19'HF) containing prymnesiophytes did not show any noticeable change in response to CO₂ enrichment. A CO₂-induced positive growth response was noticed in some diatoms (Guinardia flaccida, Cylindrotheca closterium, and Pseudo-nitzschia sp.) and dinoflagellates (Protoperidinium sp. and Peridinium sp.) indicating their efficiency to quickly acclimatize at elevated CO₂ levels. This is important to note that the positive growth response of toxigenic pennate diatoms like Pseudo-nitzschia as well as a few dinoflagellates at elevated CO₂ levels can be expected in the future-ocean scenario. The proliferation of such non-palatable phytoplankton may impact grazing, the food chain, and carbon cycling in this region.

Preference of carbon absorption determines the competitive ability of algae along atmospheric CO2 concentration

Although many studies have focused on the effects of elevated atmospheric CO₂ on algal growth, few of them have demonstrated how CO₂ interacts with carbon absorption capacity to determine the algal competition at the population level. We conducted a pairwise competition experiment of Phormidium sp., Scenedesmus quadricauda, Chlorella vulgaris and Synedra ulna. The results showed that when the CO₂ concentration increased from 400 to 760 ppm, the competitiveness of S. quadricauda increased, the competitiveness of Phormidium sp. and C. vulgaris decreased, and the competitiveness of S. ulna was always the lowest. We constructed a model to explore whether interspecific differences in affinity and flux rate for CO₂ and HCO₃ ^- could explain changes in competitiveness between algae species along the gradient of atmospheric CO₂ concentration. Affinity and flux rates are the capture capacity and transport capacity of substrate respectively, and are inversely proportional to each other. The simulation results showed that, when the atmospheric CO₂ concentration was low, species with high affinity for both CO₂ and HCO₃ ^- (HCHH) had the highest competitiveness, followed by the species with high affinity for CO₂ and low affinity for HCO₃ ^- (HCLH), the species with low affinity for CO₂ and high affinity for HCO₃ ^- (LCHH) and the species with low affinity for both CO₂ and HCO₃ ^- (LCLH); when the CO₂ concentration was high, the species were ranked according to the competitive ability: LCHH > LCLH > HCHH > HCLH. Thus, low resource concentration is beneficial to the growth and reproduction of algae with high affinity. With the increase in atmospheric CO₂ concentration, the competitive advantage changed from HCHH species to LCHH species. These results indicate the important species types contributing to water bloom under the background of increasing global atmospheric CO₂, highlighting the importance of carbon absorption characteristics in understanding, predicting and regulating population dynamics and community composition of algae.

The need for unrealistic experiments in global change biology

Climate change is an existential threat, and our ability to conduct experiments on how organisms will respond to it is limited by logistics and resources, making it vital that experiments be maximally useful. The majority of experiments on phytoplankton responses to warming and CO₂ use only two levels of each driver. However, to project the characters of future populations, we need a mechanistic and generalisable explanation for how phytoplankton respond to concurrent changes in temperature and CO₂. This requires experiments with more driver levels, to produce response surfaces that can aid in the development of predictive models. We recommend prioritising experiments or programmes that produce such response surfaces on multiple scales for phytoplankton.

Diatoms and Their Microbiomes in Complex and Changing Polar Oceans

Diatoms, a key group of polar marine microbes, support highly productive ocean ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore under constant biotic and abiotic pressures which directly influence their evolution through natural selection. Despite their importance in polar ecosystems, polar diatoms are understudied compared to temperate species. The observed rapid change in the polar climate, especially warming, has created increased research interest to discover the underlying causes and potential consequences on single species to entire ecosystems. Next-Generation Sequencing (NGS) technologies have greatly expanded our knowledge by revealing the molecular underpinnings of physiological adaptations to polar environmental conditions. Their genomes, transcriptomes, and proteomes together with the first eukaryotic meta-omics data of surface ocean polar microbiomes reflect the environmental pressures through adaptive responses such as the expansion of protein families over time as a consequence of selection. Polar regions and their microbiomes are inherently connected to climate cycles and their feedback loops. An integrated understanding built on “omics” resources centered around diatoms as key primary producers will enable us to reveal unifying concepts of microbial co-evolution and adaptation in polar oceans. This knowledge, which aims to relate past environmental changes to specific adaptations, will be required to improve climate prediction models for polar ecosystems because it provides a unifying framework of how interacting and co-evolving biological communities might respond to future environmental change.

Intraspecific variation in metal tolerance modulate competition between two marine diatoms

Despite widespread metal pollution of coastal ecosystems, little is known of its effect on marine phytoplankton. We designed a co-cultivation experiment to test if toxic dose-response relationships can be used to predict the competitive outcome of two species under metal stress. Specifically, we took into account intraspecific strain variation and selection. We used 72 h dose-response relationships to model how silver (Ag), cadmium (Cd), and copper (Cu) affect both intraspecific strain selection and competition between taxa in two marine diatoms (Skeletonema marinoi and Thalassiosira baltica). The models were validated against 10-day co-culture experiments, using four strains per species. In the control treatment, we could predict the outcome using strain-specific growth rates, suggesting low levels of competitive interactions between the species. Our models correctly predicted which species would gain a competitive advantage under toxic stress. However, the absolute inhibition levels were confounded by the development of chronic toxic stress, resulting in a higher long-term inhibition by Cd and Cu. We failed to detect species differences in average Cu tolerance, but the model accounting for strain selection accurately predicted a competitive advantage for T. baltica. Our findings demonstrate the importance of incorporating multiple strains when determining traits and when performing microbial competition experiments.

Seasonal genotype dynamics of a marine dinoflagellate: Pelagic populations are homogeneous and as diverse as benthic seed banks

Genetic diversity is the basis for evolutionary adaptation and selection under changing environmental conditions. Phytoplankton populations are genotypically diverse, can become genetically differentiated within small spatiotemporal scales and many species form resting stages. Resting stage accumulations in sediments (seed banks) are expected to serve as reservoirs for genetic information, but so far their role in maintaining phytoplankton diversity and in evolution has remained unclear. In this study we used the toxic dinoflagellate Alexandrium ostenfeldii (Dinophyceae) as a model organism to investigate if (i) the benthic seed bank is more diverse than the pelagic population and (ii) the pelagic population is seasonally differentiated. Resting stages (benthic) and plankton (pelagic) samples were collected at a coastal bloom site in the Baltic Sea, followed by cell isolation and genotyping using microsatellite markers (MS) and restriction site associated DNA sequencing (RAD). High clonal diversity (98%–100%) combined with intermediate to low gene diversity (0.58–0.03, depending on the marker) was found. Surprisingly, the benthic and pelagic fractions of the population were equally diverse, and the pelagic fraction was temporally homogeneous, despite seasonal fluctuation of environmental selection pressures. The results of this study suggest that continuous benthic–pelagic coupling, combined with frequent sexual reproduction, as indicated by persistent linkage equilibrium, prevent the dominance of single clonal lineages in a dynamic environment. Both processes harmonize the pelagic with the benthic population and thus prevent seasonal population differentiation. At the same time, frequent sexual reproduction and benthic–pelagic coupling maintain high clonal diversity in both habitats.

Restoration, conservation and phytoplankton hysteresis

Phytoplankton growth depends not only upon external factors that are not strongly altered by the presence of phytoplankton, such as temperature, but also upon factors that are strongly influenced by activity of phytoplankton, including photosynthetically active radiation, and the availability of the macronutrients carbon, nitrogen, phosphorus and, for some, silicate. Since phytoplankton therefore modify, and to an extent create, their own habitats, established phytoplankton communities can show resistance and resilience to change, including managed changes in nutrient regimes. Phytoplankton blooms and community structures can be predicted from the overall biogeochemical setting and inputs, but restorations may be influenced by the physiological responses of established phytoplankton taxa to nutrient inputs, temperature, second-order changes in illumination and nutrient recycling. In this review we discuss the contributions of phytoplankton ecophysiology to biogeochemical hysteresis and possible effects on community composition in the face of management, conservation or remediation plans.

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.

Revealing environmentally driven population dynamics of an Arctic diatom using a novel microsatellite PoolSeq barcoding approach

Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms, it is challenging to follow intraspecific dynamics over space and time. We propose a new method, microsatellite PoolSeq barcoding (MPB), for tracing allele frequency changes in protist populations. We successfully applied this method to experimental community incubations and field samples of the diatom Thalassiosira hyalina from the Arctic, a rapidly changing ecosystem. Validation of the method found compelling accuracy in comparison with established genotyping approaches within different diversity contexts. In experimental and environmental samples, we show that MPB can detect meaningful patterns of population dynamics, resolving allelic stability and shifts within a key diatom species in response to experimental treatments as well as different bloom phases and years. Through our novel MPB approach, we produced a large dataset of populations at different time-points and locations with comparably little effort. Results like this can add insights into the roles of selection and plasticity in natural protist populations under stable experimental but also variable field conditions. Especially for organisms where genotype sampling remains challenging, MPB holds great potential to efficiently resolve eco-evolutionary dynamics and to assess the mechanisms and limits of resilience to environmental stressors.

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.

Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans

Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO₂ to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO₂, which is vital information toward modeling their response to future CO₂ levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO₂ variability. The current study investigates the interlink between the environmental variability of CO₂ and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO₂ concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8-5 μm, 5-20 μm, 20-180 μm, and 180-2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO₂ levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.

Meta-analysis of multiple driver effects on marine phytoplankton highlights modulating role of pCO2

Responses of marine primary production to a changing climate are determined by a concert of multiple environmental changes, for example in temperature, light, pCO₂ , nutrients, and grazing. To make robust projections of future global marine primary production, it is crucial to understand multiple driver effects on phytoplankton. This meta-analysis quantifies individual and interactive effects of dual driver combinations on marine phytoplankton growth rates. Almost 50% of the single-species laboratory studies were excluded because central data and metadata (growth rates, carbonate system, experimental treatments) were insufficiently reported. The remaining data (42 studies) allowed for the analysis of interactions of pCO₂ with temperature, light, and nutrients, respectively. Growth rates mostly respond non-additively, whereby the interaction with increased pCO₂ profusely dampens growth-enhancing effects of high temperature and high light. Multiple and single driver effects on coccolithophores differ from other phytoplankton groups, especially in their high sensitivity to increasing pCO₂ . Polar species decrease their growth rate in response to high pCO₂ , while temperate and tropical species benefit under these conditions. Based on the observed interactions and projected changes, we anticipate primary productivity to: (a) first increase but eventually decrease in the Arctic Ocean once nutrient limitation outweighs the benefits of higher light availability; (b) decrease in the tropics and mid-latitudes due to intensifying nutrient limitation, possibly amplified by elevated pCO₂ ; and (c) increase in the Southern Ocean in view of higher nutrient availability and synergistic interaction with increasing pCO₂ . Growth-enhancing effect of high light and warming to coccolithophores, mainly Emiliania huxleyi, might increase their relative abundance as long as not offset by acidification. Dinoflagellates are expected to increase their relative abundance due to their positive growth response to increasing pCO₂ and light levels. Our analysis reveals gaps in the knowledge on multiple driver responses and provides recommendations for future work on phytoplankton.

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.

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.