Inter-individual physiological variation in responses to environmental variation and environmental change: Integrating across traits and time

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.

Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.

Copper toxicity does not affect low tide emersion tolerance of Mytilus galloprovincialis

Intertidal mussels are well adapted to withstand emersion from water during low tide, but they may be intermittently exposed to waterborne toxicants such as copper, which targets physiological processes including metabolism, ammonia excretion, and osmoregulation. To determine if copper exposure damages intertidal organisms' ability to tolerate tidal emersion, Mediterranean mussels (Mytilus galloprovincialis) were exposed to copper for 96 h followed by 6 h of emersion. Oxygen uptake increased after copper exposure which suggests that copper accumulation caused moderate stress in the mussels, but ammonia excretion and anaerobic metabolism were unaffected by mixed copper and emersion exposures. Shell composition analyses indicate that cycles of copper exposure and tidal emersion may affect bivalve shell growth, but copper deposition into shells may decrease the metal's overall toxicity. Results suggest that copper does not damage M. galloprovincialis's tolerance to tidal emersion, and insight is provided into the mussel's ability to overcome mixed stressor exposures.

A predictive timeline of wildlife population collapse

Contemporary rates of biodiversity decline emphasize the need for reliable ecological forecasting, but current methods vary in their ability to predict the declines of real-world populations. Acknowledging that stressor effects start at the individual level, and that it is the sum of these individual-level effects that drives populations to collapse, shifts the focus of predictive ecology away from using predominantly abundance data. Doing so opens new opportunities to develop predictive frameworks that utilize increasingly available multi-dimensional data, which have previously been overlooked for ecological forecasting. Here, we propose that stressed populations will exhibit a predictable sequence of observable changes through time: changes in individuals' behaviour will occur as the first sign of increasing stress, followed by changes in fitness-related morphological traits, shifts in the dynamics (for example, birth rates) of populations and finally abundance declines. We discuss how monitoring the sequential appearance of these signals may allow us to discern whether a population is increasingly at risk of collapse, or is adapting in the face of environmental change, providing a conceptual framework to develop new forecasting methods that combine multi-dimensional (for example, behaviour, morphology, life history and abundance) data.

Elevated temperature and carbon dioxide levels alter growth rates and shell composition in the fluted giant clam, Tridacna squamosa

Giant clams produce massive calcified shells with important biological (e.g., defensive) and ecological (e.g., habitat-forming) properties. Whereas elevated seawater temperature is known to alter giant clam shell structure, no study has examined the effects of a simultaneous increase in seawater temperature and partial pressure of carbon dioxide (pCO₂) on shell mineralogical composition in these species. We investigated the effects of 60-days exposure to end-of-the-century projections for seawater temperature (+ 3 °C) and pCO₂ (+ 500 µatm) on growth, mineralogy, and organic content of shells and scutes in juvenile Tridacna squamosa giant clams. Elevated temperature had no effect on growth rates or organic content, but did increase shell [²⁴Mg]/[⁴⁰Ca] as well as [⁴⁰Ca] in newly-formed scutes. Elevated pCO₂ increased shell growth and whole animal mass gain. In addition, we report the first evidence of an effect of elevated pCO₂ on element/Ca ratios in giant clam shells, with significantly increased [¹³⁷Ba]/[⁴⁰Ca] in newly-formed shells. Simultaneous exposure to both drivers greatly increased inter-individual variation in mineral concentrations and resulted in reduced shell N-content which may signal the onset of physiological stress. Overall, our results indicate a greater influence of pCO₂ on shell mineralogy in giant clams than previously recognized.

Effects of heat acclimation on cardiac function in the intertidal mussel Mytilus californianus: can laboratory-based indices predict survival in the field?

Thermal performance curves are commonly used to investigate the effects of heat acclimation on thermal tolerance and physiological performance. However, recent work indicates that the metrics of these curves heavily depend on experimental design and may be poor predictors of animal survival during heat events in the field. In intertidal mussels, cardiac thermal performance (CTP) tests have been widely used as indicators of animals' acclimation or acclimatization state, providing two indices of thermal responses: critical temperature (Tcrit; the temperature above which heart rate abruptly declines) and flatline temperature (Tflat; the temperature where heart rate ceases). Despite the wide use of CTP tests, it remains largely unknown how Tcrit and Tflat change within a single individual after heat acclimation, and whether changes in these indices can predict altered survival in the field. Here, we addressed these issues by evaluating changes in CTP indices in the same individuals before and after heat acclimation. For control mussels, merely reaching Tcrit was not lethal, whereas remaining at Tcrit for ≥10 min was lethal. Heat acclimation significantly increased Tcrit only in mussels with an initially low Tcrit (<35°C), but improved their survival time above Tcrit by 20 min on average. Tflat increased by ∼1.6°C with heat acclimation, but it is unlikely that increased Tflat improves survival in the field. In summary, Tcrit and Tflat per se may fall short of providing quantitative indices of thermal tolerance in mussels; instead, a combination of Tcrit and tolerance time at temperatures ≥Tcrit better defines changes in thermal tolerance with heat acclimation.

Environment-driven shifts in inter-individual variation and phenotypic integration within subnetworks of the mussel transcriptome and proteome

The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene‐to‐protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter‐individual variation in both transcript and protein expression levels among California mussels, Mytilus californianus Conrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean and interindividual heterogeneity of body temperature. To target a diverse set of physiological functions, we assessed variation within 19 expression subnetworks, including canonical stress‐response pathways and empirically derived coexpression clusters that represent a diffuse set of cellular processes. Variation in expression was particularly pronounced in the treatments with high mean and heterogeneous body temperatures. However, with few exceptions, environment‐dependent shifts of variation in the transcriptome were not reflected in the proteome. A metric of phenotypic integration provided evidence for a greater degree of constraint on relative expression levels (i.e., stronger correlation) within expression subnetworks in benign, homogeneous environments. Our results suggest that environments that are more stressful on average – and which also tend to be more heterogeneous – can relax these expression constraints and reduce phenotypic integration within biochemical subnetworks. Context‐dependent “unmasking” of functional variation may contribute to interindividual differences in physiological phenotype and performance in stressful environments.

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.

Embryonic thermal manipulation impacts the postnatal transcriptome response of heat-challenged Japanese quails

BACKGROUND

The thermal-manipulation (TM) during egg incubation is a cyclic exposure to hot or cold temperatures during embryogenesis that is associated to long-lasting effects on growth performance, physiology, metabolism and temperature tolerance in birds. An increase of the incubation temperature of Japanese quail eggs affected the embryonic and post-hatch survival, growth, surface temperatures and blood characteristics potentially related to thermoregulation capacities. To gain new insights in the molecular basis of TM in quails, we investigated by RNA-seq the hypothalamus transcriptome of 35 days-old male and female quails that were treated by TM or not (C, control) during embryogenesis and that were exposed (HC) or not (RT) to a 36 °C heat challenge for 7 h before sampling.

RESULTS

For males, 76, 27, 47 and 0 genes were differentially expressed in the CHC vs. CRT, CRT vs. TMRT, TMHC vs. TMRT and CHC vs. TMHC comparisons, respectively. For females, 17, 0, 342 and 1 genes were differentially expressed within the same respective comparisons. Inter-individual variability of gene expression response was observed particularly when comparing RT and HC female animals. The differential expression of several genes was corroborated by RT-qPCR analysis. Gene Ontology functional analysis of the differentially expressed genes showed a prevalent enrichment of terms related to cellular responses to stimuli and gene expression regulation in both sexes. Gene Ontology terms related to the membrane transport, the endoplasmic reticulum and mitochondrial functions as well as DNA metabolism and repair were also identified in specific comparisons and sexes.

CONCLUSIONS

TM had little to no effect on the regulation of gene expression in the hypothalamus of 35 days-old Japanese quails. However, the consequences of TM on gene expression were revealed by the HC, with sex-specific and common functions altered. The effects of the HC on gene expression were most prominent in TM females with a ~ 20-fold increase of the number of differentially expressed genes, suggesting that TM may enhance the gene response during challenging conditions in female quail hypothalamus. TM may also promote new cellular strategies in females to help coping to the adverse conditions as illustrated by the identification of differentially expressed genes related to the mitochondrial and heat-response functions.

Acclimation to future climate exposes vulnerability to cold extremes in intertidal sea hares

Highly dynamic environments like estuaries will undergo unpredictable shifts in thermal and salinity regimes with ongoing climate change. These interactive stressors fluctuate predictably and seasonally over historical periods, which has facilitated the evolution of wide environmental tolerance in some estuarine inhabitants. However, physiological and behavioral acclimatization is seasonally based for many estuarine species, meaning that a shift in the unpredictability of climate events and trends will disrupt the effectiveness of evolved tolerance mechanisms. Of particular concern are extreme cold events and high-volume precipitation events, which will acutely and unpredictably alter an estuarine habitat. The eelgrass sea hare, Phyllaplysia taylori, has documented euryhaline and eurythermal tolerance to summer conditions, but the winter environment may pose a greater challenge to seasonally relevant acclimatization scenarios. Here, we characterized lower critical thermal limits, and behavioral responses to stimuli leading up to these limits, in two central California P. taylori populations under four temperature-salinity scenarios in a laboratory acclimation experiment. Acclimation to warmer conditions significantly increased critical thermal minima, while fresher conditions resulted in high mortality. However, the surviving individuals in the fresher conditions were able to respond to stimuli more quickly overall, despite their shortest response time being at a higher temperature than the saltier-acclimated individuals. Within the environmental context of their natural habitats, we find that acclimation to climate change-induced warming will hinder sea hares' ability to weather existing and future cold extremes and precipitation events.

Mussel acclimatization to high, variable temperatures is lost slowly upon transfer to benign conditions

Climate change is increasing the temperature variability animals face, and thermal acclimatization allows animals to adjust adaptively to this variability. Although the rate of heat acclimatization has received some study, little is known about how long these adaptive changes remain without continuing exposure to heat stress. This study explored the rate at which field acclimatization states are lost when temperature variability is minimized during constant submersion. California mussels (Mytilus californianus) with different acclimatization states were collected from high- and low-zone sites (∼12 versus ∼5°C daily temperature ranges, respectively) and then kept submerged at 15°C for 8 weeks. Each week, the cardiac thermal performance of mussels was measured as a metric of acclimatization state: critical (Tcrit) and flatline (Tflat) temperatures were recorded. Over 8 weeks of constant submersion, the mean Tcrit of high-zone mussels decreased by 1.07°C from baseline, but low-zone mussels' mean Tcrit was unchanged. High- and low-zone mussels' mean maximum heart rate (HR) and resting HR decreased ∼12 and 35%, respectively. Tflat was unchanged in both groups. These data suggest that Tcrit and HR are more physiologically plastic in response to the narrowing of an animal's daily temperature range than Tflat is, and that an animal's prior acclimatization state (high versus low) influences the acclimatory capacity of Tcrit Approximately 2 months were required for the cardiac thermal performance of the high-zone mussels to reach that of the low-zone mussels, suggesting that acclimatization to high and variable temperatures may persist long enough to enable these animals to cope with intermittent bouts of heat stress.

Establishing typical values for hemocyte mortality in individual California mussels, Mytilus californianus

Hemocytes are immune cells in the hemolymph of invertebrates that play multiple roles in response to stressors; hemocyte mortality can thus serve as an indicator of overall animal health. However, previous research has often analyzed hemolymph samples pooled from several individuals, which precludes tracking individual responses to stressors over time. The ability to track individuals is important, however, because large inter-individual variation in response to stressors can confound the interpretation of pooled samples. Here, we describe protocols for analysis of inter- and intra-individual variability in hemocyte mortality across repeated hemolymph samples of California mussels, Mytilus californianus, free from typical abiotic stressors. To assess individual variability in hemocyte mortality with serial sampling, we created four groups of 15 mussels each that were repeatedly sampled four times: at baseline (time zero) and three subsequent times separated by either 24, 48, 72, or 168 h. Hemocyte mortality was assessed by fluorescence-activated cell sorting (FACS) of cells stained with propidium iodide. Our study demonstrates that hemolymph can be repeatedly sampled from individual mussels without mortality; however, there is substantial inter- and intra-individual variability in hemocyte mortality through time that is partially dependent on the sampling interval. Across repeated samples, individual mussels' hemocyte mortality had, on average, a range of ~6% and a standard deviation of ~3%, which was minimized with sampling periods ≥72 h apart. Due to this intra-individual variability, obtaining ≥2 samples from a specimen will more accurately establish an individual's baseline. Pooled-sample means were similar to individual-sample means; however, pooled samples masked the individual variation in each group. Overall, these data lay the foundation for future work exploring individual mussels' temporal responses to various stressors on a cellular level.

The cellular stress response and temperature: Function, regulation, and evolution

The cellular stress response (CSR) is critical for enabling organisms to cope with thermal damage to proteins, nucleic acids, and membranes. It is a graded response whose properties vary with the degree of cellular damage. Molecular damage has positive, as well as negative, function-perturbing effects. Positive effects include crucial regulatory interactions that orchestrate involvement of the different components of the CSR. Thermally unfolded proteins signal for rapid initiation of transcription of genes encoding heat shock proteins (HSPs), central elements of the heat shock response (HSR). Thermal disruption of messenger RNA (mRNA) secondary structures in untranslated regions leads to the culling of the mRNA pool: thermally labile mRNAs for housekeeping proteins are degraded by exonucleases; heat-resistant mRNAs for stress proteins like HSPs then can monopolize the translational apparatus. Thus, proteins and RNA function as "cellular thermometers," and evolved differences in their thermal stabilities enable rapid initiation of the CSR whenever cell temperature rises significantly above the normal thermal range of a species. Covalent DNA damage, which may result from increased production of reactive oxygen species, is temperature-dependent; its extent may determine cellular survival. High levels of stress that exceed capacities for molecular repair can lead to proteolysis, inhibition of cell division, and programmed cell death (apoptosis). Onset of these processes may occur later in the stress period, after initiation of the HSR, to allow HSPs opportunity to restore protein homeostasis. Delay of these energy costly processes may also result from shortfalls in availability of adenosine triphosphate and reducing power during times of peak stress.