The Physiology and Ecology of Diapause in Marine Copepods

Revealing the profound influence of diapause on gene expression: Insights from the annual transcriptome of the copepod Calanus finmarchicus

Annual rhythms are observed in living organisms with numerous ecological implications. In the zooplanktonic copepod Calanus finmarchicus, such rhythms are crucial regarding its phenology, body lipid accumulation, and global carbon storage. Climate change drives annual biological rhythms out of phase with the prevailing environmental conditions with yet unknown but potentially catastrophic consequences. However, the molecular dynamics underlying phenology are still poorly described. In a rhythmic analysis of C. finmarchicus annual gene expression, results reveal that more than 90% of the transcriptome shows significant annual rhythms, with abrupt and dramatic upheaval between the active and diapause life cycle states. This work explores the implication of the circadian clock in the annual timing, which may control epigenetic mechanisms to profoundly modulate gene expression in response to calendar time. Results also suggest an increased light sensitivity during diapause that would ensure the photoperiodic entrainment of the endogenous annual clock.

Effects of petrogenic pollutants on North Atlantic and Arctic Calanus copepods: From molecular mechanisms to population impacts

Oil and gas industries in the Northern Atlantic Ocean have gradually moved closer to the Arctic areas, a process expected to be further facilitated by sea ice withdrawal caused by global warming. Copepods of the genus Calanus hold a key position in these cold-water food webs, providing an important energetic link between primary production and higher trophic levels. Due to their ecological importance, there is a concern about how accidental oil spills and produced water discharges may impact cold-water copepods. In this review, we summarize the current knowledge of the toxicity of petroleum on North Atlantic and Arctic Calanus copepods. We also review how recent development of high-quality transcriptomes from RNA-sequencing of copepods have identified genes regulating key biological processes, like molting, diapause and reproduction in Calanus copepods, to suggest linkages between exposure, molecular mechanisms and effects on higher levels of biological organization. We found that the available ecotoxicity threshold data for these copepods provide valuable information about their sensitivity to acute petrogenic exposures; however, there is still insufficient knowledge regarding underlying mechanisms of toxicity and the potential for long-term implications of relevance for copepod ecology and phenology. Copepod transcriptomics has expanded our understanding of how key biological processes are regulated in cold-water copepods. These advances can improve our understanding of how pollutants affect biological processes, and thus provide the basis for new knowledge frameworks spanning the effect continuum from molecular initiating events to adverse effects of regulatory relevance. Such efforts, guided by concepts such as adverse outcome pathways (AOPs), enable standardized and transparent characterization and evaluation of knowledge and identifies research gaps and priorities. This review suggests enhancing mechanistic understanding of exposure-effect relationships to better understand and link biomarker responses to adverse effects to improve risk assessments assessing ecological effects of pollutant mixtures, like crude oil, in Arctic areas.

A transcriptomic examination of encased rotifer embryos reveals the developmental trajectory leading to long-term dormancy; are they "animal seeds"?

BACKGROUND

Organisms from many distinct evolutionary lineages acquired the capacity to enter a dormant state in response to environmental conditions incompatible with maintaining normal life activities. Most studied organisms exhibit seasonal or annual episodes of dormancy, but numerous less studied organisms enter long-term dormancy, lasting decades or even centuries. Intriguingly, many planktonic animals produce encased embryos known as resting eggs or cysts that, like plant seeds, may remain dormant for decades. Herein, we studied a rotifer Brachionus plicatilis as a model planktonic species that forms encased dormant embryos via sexual reproduction and non-dormant embryos via asexual reproduction and raised the following questions: Which genes are expressed at which time points during embryogenesis? How do temporal transcript abundance profiles differ between the two types of embryos? When does the cell cycle arrest? How do dormant embryos manage energy?

RESULTS

As the molecular developmental kinetics of encased embryos remain unknown, we employed single embryo RNA sequencing (CEL-seq) of samples collected during dormant and non-dormant embryogenesis. We identified comprehensive and temporal transcript abundance patterns of genes and their associated enriched functional pathways. Striking differences were uncovered between dormant and non-dormant embryos. In early development, the cell cycle-associated pathways were enriched in both embryo types but terminated with fewer nuclei in dormant embryos. As development progressed, the gene transcript abundance profiles became increasingly divergent between dormant and non-dormant embryos. Organogenesis was suspended in dormant embryos, concomitant with low transcript abundance of homeobox genes, and was replaced with an ATP-poor preparatory phase characterized by very high transcript abundance of genes encoding for hallmark dormancy proteins (e.g., LEA proteins, sHSP, and anti-ROS proteins, also found in plant seeds) and proteins involved in dormancy exit. Surprisingly, this period appeared analogous to the late maturation phase of plant seeds.

CONCLUSIONS

The study highlights novel divergent temporal transcript abundance patterns between dormant and non-dormant embryos. Remarkably, several convergent functional solutions appear during the development of resting eggs and plant seeds, suggesting a similar preparatory phase for long-term dormancy. This study accentuated the broad novel molecular features of long-term dormancy in encased animal embryos that behave like "animal seeds".

Adaptation and Survival of Marine-Associated Spiders (Araneae)

Aquatic environments are an unusual habitat for most arthropods. Nevertheless, many arthropod species that were once terrestrial dwelling have transitioned back to marine and freshwater environments, either as semiaquatic or, more rarely, as fully aquatic inhabitants. Transition to water from land is exceptional, and without respiratory modifications to allow for extended submergence and the associated hypoxic conditions, survival is limited. In this article, we review marine-associated species that have made this rare transition in a generally terrestrial group, spiders. We include several freshwater spider species for comparative purposes. Marine-associated spiders comprise less than 0.3% of spider species worldwide but are found in over 14% of all spider families. As we discuss, these spiders live in environments that, with tidal action, hydraulic forces, and saltwater, are more extreme than freshwater habitats, often requiring physiological and behavioral adaptations to survive. Spiders employ many methods to survive inundation from encroaching tides, such as air bubble respiration, airtight nests, hypoxic comas, and fleeing incoming tides. While airway protection is the primary survival strategy, further survival adaptations include saltwater-induced osmotic regulation, dietary composition, predator avoidance, reproduction, locomotory responses, and adaptation to extreme temperatures and hydrostatic pressures that challenge existence in marine environments.

Post-Diapause DNA Replication during Oogenesis in a Capital-Breeding Copepod

In high-latitude environments where seasonal changes include periods of harsh conditions, many arthropods enter diapause, a period of dormancy that is hormonally regulated. Diapause is characterized by very low metabolism, resistance to environmental stress, and developmental arrest. It allows an organism to optimize the timing of reproduction by synchronizing offspring growth and development with periods of high food availability. In species that enter dormancy as pre-adults or adults, termination of diapause is marked by the resumption of physiological processes, an increase in metabolic rates and once transitioned into adulthood for females, the initiation of oogenesis. In many cases, individuals start feeding again and newly acquired resources become available to fuel egg production. However, in the subarctic capital-breeding copepod Neocalanus flemingeri, feeding is decoupled from oogenesis. Thus, optimizing reproduction limited by fixed resources such that all eggs are of high quality and fully-provisioned, requires regulation of the number of oocytes. However, it is unknown if and how this copepod limits oocyte formation. In this study, the phase in oocyte production by post-diapause females that involved DNA replication in the ovary and oviducts was examined using incubation in 5-Ethynyl-2'-deoxyuridine (EdU). Both oogonia and oocytes incorporated EdU, with the number of EdU-labeled cells peaking at 72 hours following diapause termination. Cell labeling with EdU remained high for two weeks, decreasing thereafter with no labeling detected by four weeks post diapause, and three to four weeks before spawning of the first clutch of eggs. The results suggest that oogenesis is sequential in N. flemingeri with formation of new oocytes starting within 24 hours of diapause termination and limited to the first few weeks. Lipid consumption during diapause was minimal and relatively modest initially. This early phase in the reproductive program precedes mid-oogenesis and vitellogenesis 2, when oocytes increase in size and accumulate yolk and lipid reserves. By limiting DNA replication to the initial phase, the females effectively separate oocyte production from oocyte provisioning. A sequential oogenesis is unlike the income-breeder strategy of most copepods in which oocytes at all stages of maturation are found concurrently in the reproductive structures.

De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes

This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. 'Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study's primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive.

Rare earth element uptake mechanisms in plankton in the Estuary and Gulf of St. Lawrence

The global shift toward green energy alternatives escalates demands for new resources, including rare earth elements (REEs), as per their implications in various green innovations. However, our understanding of their environmental cycle, especially the interactions with aquatic organisms, remains deficient, ultimately hindering environmental protection efforts. Here, we investigate the accumulation of REEs and 18 other elements in bulk and sorted plankton collected with different net mesh sizes (30, 63, 200, 333, 500 μm) in the Estuary and Gulf of St. Lawrence in the summer and winter of 2020. We observed significant correlations between the concentrations of REEs and elements of different charge numbers and ionic radii (Ba, Co, Cs, Fe, Mn, Pb, Rb and V), indicating non-selective uptake of REEs into plankton. All these elements have their highest concentrations in the fluvial corridor and upper estuary, with more significant enrichment in phytoplankton ([La] = 26.4 ± 4.8 mg kg^-1) than zooplankton ([La] = 11.6 ± 8.3 mg kg^-1). Their concentrations decrease to the minimum in the Gulf of St. Lawrence, especially in zooplankton ([La] = 4.8 × 10^-2 ± 3.2 × 10^-2 mg kg^-1). We also assessed REE patterns to identify differential REE fractionation processes and anomalies. The freshwater plankton exhibits enrichment of middle REEs (MREEs) relative to the light and heavy REEs (LREEs and HREEs), potentially because of the higher binding affinity of MREEs on cellular surface transporters and metal loading effects. In estuarine and marine settings, the REE patterns in biological samples align with suspended particles, exhibiting a linear trend with LREE enrichment. This process is more noticeable in sorted macrozooplankton, which have significant Eu anomalies (Eu/Eu* up to 2), indicating differential incorporation of REEs into the chitin shells. This study highlights the significant enrichment of REEs into freshwater primary producers and the accumulation pathway similar to other inorganic elements.

Rhythms and Clocks in Marine Organisms

The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.

Machine learning techniques to characterize functional traits of plankton from image data

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.

Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus

The copepod Calanus finmarchicus (Crustacea, Copepoda) is a key zooplanktonic species with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to cope with long periods of limited food supply, while growth and reproduction are timed to take advantage of seasonal peaks in primary production. However, anthropogenic warming is inducing changes in the expected timing of phytoplankton blooms, suggesting phenological mismatches with negative consequences for the N. Atlantic ecosystem. While diapause mechanisms are mainly studied in terrestrial arthropods, specifically on laboratory model species, such as the fruit fly Drosophila, the molecular investigations of annual rhythms in wild marine species remain fragmentary. Here we performed a rigorous year‐long monthly sampling campaign of C. finmarchicus in a Scottish Loch (UK; 56.45°N, 5.18°W) to generate an annual transcriptome. The mRNA of 36 samples (monthly triplicate of 25 individuals) have been deeply sequenced with an average depth of 137 ± 4 million reads (mean ± SE) per sample, aligned to the reference transcriptome, and filtered. We detail the quality assessment of the datasets and provide a high‐quality resource for the investigation of wild annual transcriptomic rhythms (35,357 components) in a key diapausing zooplanktonic species.

Physiological Acclimatization in High-Latitude Zooplankton

How individual organisms adapt to non-optimal conditions through physiological acclimatization is central to predicting the consequences of unusual abiotic and biotic conditions such as those produced by marine heat waves. The Northeast Pacific, including the Gulf of Alaska experienced an extreme warming event (2014-2016, "The Blob") that affected all trophic levels leading to large-scale changes in the community. The marine copepod Neocalanus flemingeri is one key member of the subarctic Pacific pelagic ecosystem. During the spring phytoplankton bloom this copepod builds substantial lipid stores as it prepares for its non-feeding adult phase. A three-year comparison of gene expression profiles of copepods collected in Prince William Sound in the Gulf of Alaska between 2015 and 2017 included two high-temperature years (2015 and 2016) and one year with very low phytoplankton abundances (2016). The largest differences in gene expression were between high and low chlorophyll years, and not between warm and cool years. The observed gene expression patterns were indicative of physiological acclimatization. The predominant signal in 2016 was the down-regulation of genes involved in glycolysis and its incoming pathways, consistent with the modulation of metabolic rates in response to prolonged low food conditions. Despite the down-regulation of genes involved in metabolism, there was no evidence of suppression of protein synthesis based on gene expression or behavioral activity. Genes involved in muscle function were up-regulated, and the copepods were actively swimming and responsive to stimuli at collection. However, genes involved in fatty acid metabolism were down-regulated in 2016, suggesting reduced lipid accumulation.

Predicting responses to marine heatwaves using functional traits

Marine heatwaves (MHWs), discrete but prolonged periods of anomalously warm seawater, can fundamentally restructure marine communities and ecosystems. Although our understanding of these events has improved in recent years, key knowledge gaps hinder our ability to predict how MHWs will affect patterns of biodiversity. Here, we outline a functional trait approach that enables a better understanding of which species and communities will be most vulnerable to MHWs, and how the distribution of species and composition of communities are likely to shift through time. Our perspective allows progress toward unifying extreme events and longer term environmental trends as co-drivers of ecological change, with the incorporation of species traits into our predictions allowing for a greater capacity to make management decisions.

Post-diapause transcriptomic restarts: insight from a high-latitude copepod

Background

Diapause is a seasonal dormancy that allows organisms to survive unfavorable conditions and optimizes the timing of reproduction and growth. Emergence from diapause reverses the state of arrested development and metabolic suppression returning the organism to an active state. The physiological mechanisms that regulate the transition from diapause to post-diapause are still unknown. In this study, this transition has been characterized for the sub-arctic calanoid copepod Neocalanus flemingeri, a key crustacean zooplankter that supports the highly productive North Pacific fisheries. Transcriptional profiling of females, determined over a two-week time series starting with diapausing females collected from > 400 m depth, characterized the molecular mechanisms that regulate the post-diapause trajectory.

Results

A complex set of transitions in relative gene expression defined the transcriptomic changes from diapause to post-diapause. Despite low temperatures (5–6 °C), the switch from a “diapause” to a “post-diapause” transcriptional profile occurred within 12 h of the termination stimulus. Transcriptional changes signaling the end of diapause were activated within one-hour post collection and included the up-regulation of genes involved in the 20E cascade pathway, the TCA cycle and RNA metabolism in combination with the down-regulation of genes associated with chromatin silencing. By 12 h, females exhibited a post-diapause phenotype characterized by the up-regulation of genes involved in cell division, cell differentiation and multiple developmental processes. By seven days post collection, the reproductive program was fully activated as indicated by up-regulation of genes involved in oogenesis and energy metabolism, processes that were enriched among the differentially expressed genes.

Conclusions

The analysis revealed a finely structured, precisely orchestrated sequence of transcriptional changes that led to rapid changes in the activation of biological processes paving the way to the successful completion of the reproductive program. Our findings lead to new hypotheses related to potentially universal mechanisms that terminate diapause before an organism can resume its developmental program.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07557-7.

Two hundred years of zooplankton vertical migration research

Vertical migration is a geographically and taxonomically widespread behaviour among zooplankton that spans across diel and seasonal timescales. The shorter-term diel vertical migration (DVM) has a periodicity of up to 1 day and was first described by the French naturalist Georges Cuvier in 1817. In 1888, the German marine biologist Carl Chun described the longer-term seasonal vertical migration (SVM), which has a periodicity of ca. 1 year. The proximate control and adaptive significance of DVM have been extensively studied and are well understood. DVM is generally a behaviour controlled by ambient irradiance, which allows herbivorous zooplankton to feed in food-rich shallower waters during the night when light-dependent (visual) predation risk is minimal and take refuge in deeper, darker waters during daytime. However, DVMs of herbivorous zooplankton are followed by their predators, producing complex predator-prey patterns that may be traced across multiple trophic levels. In contrast to DVM, SVM research is relatively young and its causes and consequences are less well understood. During periods of seasonal environmental deterioration, SVM allows zooplankton to evacuate shallower waters seasonally and take refuge in deeper waters often in a state of dormancy. Both DVM and SVM play a significant role in the vertical transport of organic carbon to deeper waters (biological carbon sequestration), and hence in the buffering of global climate change. Although many animal migrations are expected to change under future climate scenarios, little is known about the potential implications of global climate change on zooplankton vertical migrations and its impact on the biological carbon sequestration process. Further, the combined influence of DVM and SVM in determining zooplankton fitness and maintenance of their horizontal (geographic) distributions is not well understood. The contrasting spatial (deep versus shallow) and temporal (diel versus seasonal) scales over which these two migrations occur lead to challenges in studying them at higher spatial, temporal and biological resolution and coverage. Extending the largely population-based vertical migration knowledge base to individual-based studies will be an important way forward. While tracking individual zooplankton in their natural habitats remains a major challenge, conducting trophic-scale, high-resolution, year-round studies that utilise emerging field sampling and observation techniques, molecular genetic tools and computational hardware and software will be the best solution to improve our understanding of zooplankton vertical migrations.

Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod

Many arthropods undergo a seasonal dormancy termed "diapause" to optimize timing of reproduction in highly seasonal environments. In the North Atlantic, the copepod Calanus finmarchicus completes one to three generations annually with some individuals maturing into adults, while others interrupt their development to enter diapause. It is unknown which, why and when individuals enter the diapause program. Transcriptomic data from copepods on known programs were analyzed using dimensionality reduction of gene expression and functional analyses to identify program-specific genes and biological processes. These analyses elucidated physiological differences and established protocols that distinguish between programs. Differences in gene expression were associated with maturation of individuals on the reproductive program, while those on the diapause program showed little change over time. Only two of six filters effectively separated copepods by developmental program. The first one included all genes annotated to RNA metabolism and this was confirmed using differential gene expression analysis. The second filter identified 54 differentially expressed genes that were consistently up-regulated in individuals on the diapause program in comparison with those on the reproductive program. Annotated to oogenesis, RNA metabolism and fatty acid biosynthesis, these genes are both indicators for diapause preparation and good candidates for functional studies.

What Is the Storage Effect, Why Should It Occur in Cancers, and How Can It Inform Cancer Therapy?

Intratumor heterogeneity is a feature of cancer that is associated with progression, treatment resistance, and recurrence. However, the mechanisms that allow diverse cancer cell lineages to coexist remain poorly understood. The storage effect is a coexistence mechanism that has been proposed to explain the diversity of a variety of ecological communities, including coral reef fish, plankton, and desert annual plants. Three ingredients are required for there to be a storage effect: (1) temporal variability in the environment, (2) buffered population growth, and (3) species-specific environmental responses. In this article, we argue that these conditions are observed in cancers and that it is likely that the storage effect contributes to intratumor diversity. Data that show the temporal variation within the tumor microenvironment are needed to quantify how cancer cells respond to fluctuations in the tumor microenvironment and what impact this has on interactions among cancer cell types. The presence of a storage effect within a patient’s tumors could have a substantial impact on how we understand and treat cancer.

De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression

Copepods are small crustaceans that dominate most zooplankton communities in terms of both abundance and biomass. In the polar oceans, a subset of large lipid-storing copepods occupy central positions in the food web because of their important role in linking phytoplankton and microzooplankton with higher trophic levels. In this paper, we generated a high-quality de novo transcriptome for Rhincalanus gigas, the largest-and among the most abundant-of the Southern Ocean copepods. We then conducted transcriptional profiling to characterize the developmental transition between late-stage juveniles and adult females. We found that juvenile R. gigas substantially upregulate lipid synthesis and glycolysis pathways relative to females, as part of a developmental gene expression program that also implicates processes such as muscle growth, chitin formation, and ion transport. This study provides the first transcriptional profile of a developmental transition within Rhincalanus gigas or any endemic Southern Ocean copepod, thereby extending our understanding of copepod molecular physiology.

Lipid metabolism in Calanus finmarchicus is sensitive to variations in predation risk and food availability

Late developmental stages of the marine copepods in the genus Calanus can spend extended periods in a dormant stage (diapause) that is preceded by the accumulation of large lipid stores. We assessed how lipid metabolism during development from the C4 stage to adult is altered in response to predation risk and varying food availability, to ultimately understand more of the metabolic processes during development in Calanus copepods. We used RNA sequencing to assess if perceived predation risk in combination with varied food availability affects expression of genes associated with lipid metabolism and diapause preparation in C. finmarchicus. The lipid metabolism response to predation risk differed depending on food availability, time and life stage. Predation risk caused upregulation of lipid catabolism with high food, and downregulation with low food. Under low food conditions, predation risk disrupted lipid accumulation. The copepods showed no clear signs of diapause preparation, supporting earlier observations of the importance of multiple environmental cues in inducing diapause in C. finmarchicus. This study demonstrates that lipid metabolism is a sensitive endpoint for the interacting environmental effects of predation pressure and food availability. As diapause may be controlled by lipid accumulation, our findings may contribute towards understanding processes that can ultimately influence diapause timing.

Bowhead whales use two foraging strategies in response to fine-scale differences in zooplankton vertical distribution

As zooplanktivorous predators, bowhead whales (Balaena mysticetus) must routinely locate patches of prey that are energy-rich enough to meet their metabolic needs. However, little is known about how the quality and quantity of prey might influence their feeding behaviours. We addressed this question using a new approach that included: (1) multi-scale biologging and unmanned aerial system observations of bowhead whales in Cumberland Sound, Nunavut (Canada), and (2) an optical plankton counter (OPC) and net collections to identify and enumerate copepod prey species through the water column. The OPC data revealed two prey layers comprised almost exclusively of lipid-rich calanoid copepods. The deep layer contained fewer, but larger, particles (10% greater overall biomass) than the shallow prey layer. Dive data indicated that the whales conducted long deep Square-shaped dives (80% of dives; averaging depth of 260.4 m) and short shallow Square-shaped dives (16%; averaging depth of 22.5 m) to feed. The whales tended to dive proportionally more to the greater biomass of zooplankton that occurred at depth. Combining behavioural recordings with prey sampling showed a more complex feeding ecology than previously understood, and provides a means to evaluate the energetic balance of individuals under current environmental conditions.

Genetic differentiation underlies seasonal variation in thermal tolerance, body size, and plasticity in a short-lived copepod

Organisms experience variation in the thermal environment on several different temporal scales, with seasonality being particularly prominent in temperate regions. For organisms with short generation times, seasonal variation is experienced across, rather than within, generations. How this affects the seasonal evolution of thermal tolerance and phenotypic plasticity is understudied, but has direct implications for the thermal ecology of these organisms. Here we document intra-annual patterns of thermal tolerance in two species of Acartia copepods (Crustacea) from a highly seasonal estuary, showing strong variation across the annual temperature cycle. Common garden, split-brood experiments indicate that this seasonal variation in thermal tolerance, along with seasonal variation in body size and phenotypic plasticity, is likely affected by genetic polymorphism. Our results show that adaptation to seasonal variation is important to consider when predicting how populations may respond to ongoing climate change.

The β-oxidation pathway is downregulated during diapause termination in Calanus copepods

Calanus copepods are keystone species in marine ecosystems, mainly due to their high lipid content, which is a nutritious food source for e.g. juvenile fish. Accumulated lipids are catabolized to meet energy requirements during dormancy (diapause), which occurs during the last copepodite stage (C5). The current knowledge of lipid degradation pathways during diapause termination is limited. We characterized changes in lipid fullness and generated transcriptional profiles in C5s during termination of diapause and progression towards adulthood. Lipid fullness of C5s declined linearly during developmental progression, but more β-oxidation genes were upregulated in early C5s compared to late C5s and adults. We identified four possible master regulators of energy metabolism, which all were generally upregulated in early C5s, compared to late C5s and adults. We discovered that one of two enzymes in the carnitine shuttle is absent from the calanoid copepod lineage. Based on the geographical location of the sampling site, the field-samples were initially presumed to consist of C. finmarchicus. However, the identification of C. glacialis in some samples underlines the need for performing molecular analyses to reliably identify Calanus species. Our findings contributes to a better understanding of molecular events occurring during diapause and diapause termination in calanoid copepods.

Diapause within the Context of Life-History Strategies in Calanid Copepods (Calanoida: Crustacea)

Post-embryonic diapause in copepods is an adaptation that allows species in the copepod family Calanidae to thrive in high-latitude environments by transforming a short spring phytoplankton bloom into large numbers of lipid-rich individuals capable of surviving a long period of starvation. The copepods, with their high-energy lipid reservoirs, are a critical food source for higher trophic levels, making the Calanidae a key component of high-latitude marine ecosystems. The physiological ecology of the developmental program remains poorly understood. However, new studies using high-throughput RNA sequencing approaches are giving detailed access to physiological status by generating gene expression profiles for both field-collected and laboratory-incubated individuals. These are beginning to characterize the diapause phenotype, elucidate the transcriptional and physiological progression through the diapause program, and illustrate the effects of organism-environment interactions. This paper reviews gene expression profiling studies on the life cycle and diapause program of Neocalanus flemingeri Miller (1988) that were conducted as part of a long-term observation program in the northern Gulf of Alaska. It summarizes recent findings and relates them to the ecology of this species and to that of other calanids.

Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals

Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estivation, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common "toolkit" of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Noncoding RNAs, especially microRNAs, are well-known regulators of biological processes associated with numerous dormancy-related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and environmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their involvement in regulating dormancy.

Pan-Arctic Depth Distribution of Diapausing Calanus Copepods

Diapause at depth is considered an integral part of the life cycle of Calanus copepods, but few studies have focused on the Arctic species Calanus glacialis and Calanus hyperboreus. By analyzing a large set of pan-arctic observational data compiled from multiple sources, we show that Arctic Calanus has a broad depth distribution in winter, indicating that diapause at depth is a facultative strategy. Both species' vertical distributions tend to deepen in winter and to be deeper and broader with increasing bottom depth, while individuals are aggregated closer to the sea floor in shallow areas. These results indicate that Arctic Calanus species pursue a relatively deep diapause habitat but are topographically blocked on the shelves. Interspecific differences in depth distribution during diapause suggest the importance of predation. The larger C. hyperboreus has a deeper diapause depth than C. glacialis, potentially to alleviate predation pressure or as a result of predation loss near the surface. Moreover, the mean depth of C. hyperboreus in winter is negatively associated with latitude, indicating a shoaling of the diapause population in the central Arctic Ocean where predation pressure is lower. Our results suggest a complex diapause behavior by Arctic Calanus, with implications for our view of the species' roles in Arctic ecosystems.

A Crude Awakening: Effects of Crude Oil on Lipid Metabolism in Calanoid Copepods Terminating Diapause

Calanus finmarchicus and Calanus glacialis are keystone zooplankton species in North Atlantic and Arctic marine ecosystems because they form a link in the trophic transfer of nutritious lipids from phytoplankton to predators on higher trophic levels. These calanoid copepods spend several months of the year in deep waters in a dormant state called diapause, after which they emerge in surface waters to feed and reproduce during the spring phytoplankton bloom. Disruption of diapause timing could have dramatic consequences for marine ecosystems. In the present study, Calanus C5 copepodites were collected in a Norwegian fjord during diapause and were subsequently experimentally exposed to the water-soluble fraction of a naphthenic North Sea crude oil during diapause termination. The copepods were sampled repeatedly while progressing toward adulthood and were analyzed for utilization of lipid stores and for differential expression of genes involved in lipid metabolism. Our results indicate that water-soluble fraction exposure led to a temporary pause in lipid catabolism, suggested by (i) slower utilization of lipid stores in water-soluble fraction-exposed C5 copepodites and (ii) more genes in the β-oxidation pathway being downregulated in water-soluble fraction-exposed C5 copepodites than in the control C5 copepodites. Because lipid content and/or composition may be an important trigger for termination of diapause, our results imply that the timing of diapause termination and subsequent migration to the surface may be delayed if copepods are exposed to oil pollution during diapause or diapause termination. This delay could have detrimental effects on ecosystem dynamics.

Copepod Embryonic Dormancy: "An Egg Is Not Just an Egg"

Long-lasting embryonic dormancy in invertebrates defies our understanding of what constitutes life because, for example, eggs of some copepods can delay hatching for decades or even centuries. Copepods, often millimeter-sized crustaceans, are some of the most numerous multicellular organisms on earth and are key organisms in most aquatic food webs. Some important free-living marine and estuarine species overwinter or oversummer by arrested embryogenesis in dormancy. The present contribution discusses the complex mechanisms behind embryonic dormancy by compiling knowledge from the 42 calanoid copepods from the superfamily Centropagoidea with well-described embryonic dormancy, which has been of scientific interest for decades. However, the determination of categories of copepod resting eggs-that is, diapause and quiescence, transitions between categories, the mechanisms controlling arrested development by the embryos, and how they interact with their surroundings-is not fully understood. Moreover, a clear link between the presence of the free-swimming population and their resting eggs in sediments is still not convincingly demonstrated. Here I evaluate the relative significance of potential cues driving the production of and the phase shift between egg categories. Understanding the initiation and termination of embryonic dormancy is of great importance for fundamental science-that is, population and food web ecology as well as climate science, aquaculture live feed, and ballast water research. Molecular techniques are developing rapidly, especially within health sciences, thus providing relevant tools applicable for plankton research. Here I suggest that applying molecular methods in addition to traditional physiological approaches in future research will lead to greater understanding of copepod embryonic dormancy, one of nature's wonders.

Response to salinity and temperature changes in the alien Asian copepod Pseudodiaptomus marinus introduced in the Black Sea

The salinity tolerance and the effect of temperature were studied on the behavior and motor activity of the nonindigenous Indo-Pacific calanoid copepod Pseudodiaptomus marinus, first found in Sevastopol Bay (Black Sea) in autumn 2016. According to the index of median lethal salinity (LS₅₀ ), the salinity tolerance range of adult P. marinus collected at 18.0 psu in November 2016 and subsequently reared in the laboratory amounted to 5.0-44.0 psu, independently of the acclimation regime. Females of P. marinus collected in December 2016 at 12.0°C became torpid at 8.0°C, a value typical of winter-spring Black Sea coastal areas. An increase in temperature from 8.0°C to 27.0°C led to an increase in the beat frequency of mouth appendages, swimming speed, and time spent cruising. However, at the same high temperature, the mean cruising speed in the feeding-current feeder P. marinus was 2-fold lower than that of the native, similarly sized cruise feeder Pseudocalanus elongatus. On the contrary, mouthpart beat frequency while cruising was 2-fold higher reaching 80 Hz, due to the creation of feeding currents in P. marinus. The results of our experiments confirm the euryhaline character of P. marinus, and point to an apparent ability to survive cold temperatures in a torpid state. This suggests the possibility of entering an overwintering stage to survive the adverse cold winter-spring environmental conditions of the Black Sea, similarly to the recent thermophilic Indo-Pacific invader Oithona davisae which established a successful population in the same area.

Eggs of the copepod Acartia tonsa Dana require hypoxic conditions to tolerate prolonged embryonic development arrest

BACKGROUND

Copepods make up the largest zooplankton biomass in coastal areas and estuaries and are pivotal for the normal development of fish larva of countless species. During spring in neritic boreal waters, the copepod pelagic biomass increases rapidly from near absence during winter. In the calanoid species Acartia tonsa, a small fraction of eggs are dormant regardless of external conditions and this has been hypothesized to be crucial for sediment egg banks and for the rapid biomass increase during spring. Other eggs can enter a state of induced arrest called quiescence when external conditions are unfavourable. While temperature is known to be a pivotal factor in the transition from developing to resting eggs and back, the role of pH and free Oxygen in embryo development has not been systematically investigated.

RESULTS

Here, we show in a laboratory setting that hypoxic conditions are necessary for resting eggs to maintain a near-intact rate of survival after several months of induced resting. We further investigate the influence of pH that is realistic for natural sediments on the viability of resting eggs and document the effect that eggs have on the pH of the surrounding environment. We find that resting eggs acidify their immediate surroundings and are able to survive in a wide range of pH.

CONCLUSIONS

This is the first study to demonstrate the importance of hypoxia on the survival capabilities of A. tonsa resting eggs in a controlled laboratory setting, and the first to show that the large majority of quiescent eggs are able to tolerate prolonged resting. These findings have large implications for the understanding of the recruitment of copepods from sediment egg banks, which are considered the primary contributor of nauplii seeded to pelagic populations in nearshore habitats in late spring.

Physiological characterization of the emergence from diapause: A transcriptomics approach

Organisms inhabiting high-latitude environments have evolved adaptations, such as diapause to time reproduction and growth to optimize their survival. However, the physiological regulation of the timing of complex life histories is poorly understood, particularly for marine copepods, that diapause at depth. A member of the pelagic community of the sub-Arctic Pacific Ocean, Neocalanus flemingeri enters diapause in June. Egg production occurs in winter/spring. In order to characterize the transition from diapause to egg release, females were collected in late September from 400-700 m depth, incubated in the dark at 4-5 °C and sampled for RNASeq at weekly intervals. The diapause phenotype showed down-regulation of protein turnover and up-regulation of stress genes. Activation of the reproductive program was marked by the up-regulation of genes involved in germline development. Thereafter, progress through phases of oocyte development could be linked to changes in gene expression. At 5 weeks, females showed up-regulation of spermatogenesis, indicating that stored sperm had been in a quiescent stage and completed their maturation inside the female. Gene expression profiles provide a framework to stage field-collected females. The 7-week progression from diapause to late oogenesis suggests that females typically spawning in January initiated the reproductive program in November.

Stress tolerance in diapausing embryos of Artemia franciscana is dependent on heat shock factor 1 (Hsf1)

Embryos of the crustacean, Artemia franciscana, may undergo oviparous development, forming encysted embryos (cysts) that are released from females and enter diapause, a state of suppressed metabolism and greatly enhanced stress tolerance. Diapause-destined embryos of A. franciscana synthesize three small heat shock proteins (sHsps), p26, ArHsp21 and ArHsp22, as well as artemin, a ferritin homologue, all lacking in embryos that develop directly into nauplii. Of these diapause-specific molecular chaperones, p26 and artemin are important contributors to the extraordinary stress tolerance of A. franciscana cysts, but how their synthesis is regulated is unknown. To address this issue, a cDNA for heat shock factor 1 (Hsf1), shown to encode a protein similar to Hsf1 from other organisms, was cloned from A. franciscana. Hsf1 was knocked down by RNA interference (RNAi) in nauplii and cysts of A. franciscana. Nauplii lacking Hsf1 died prematurely upon release from females, showing that this transcription factor is essential to the survival of nauplii. Diapause cysts with diminished amounts of Hsf1 were significantly less stress tolerant than cysts containing normal levels of Hsf1. Moreover, cysts deficient in Hsf1 possessed reduced amounts of p26, ArHsp21, ArHsp22 and artemin, revealing dependence on Hsf1 for expression of their genes and maximum stress tolerance. The results demonstrate an important role for Hsf1, likely in concert with other transcription factors, in the survival and growth of A. franciscana and in the developmentally regulated synthesis of proteins responsible for the stress tolerance of diapausing A. franciscana cysts.

Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology

Copepods harbor diverse bacterial communities, which collectively carry out key biogeochemical transformations in the ocean. However, bulk copepod sampling averages over the variability in their associated bacterial communities, thereby limiting our understanding of the nature and specificity of copepod-bacteria associations. Here, we characterize the bacterial communities associated with nearly 200 individual Calanus finmarchicus copepods transitioning from active growth to diapause. We find that all individual copepods sampled share a small set of "core" operational taxonomic units (OTUs), a subset of which have also been found associated with other marine copepod species in different geographic locations. However, most OTUs are patchily distributed across individual copepods, thereby driving community differences across individuals. Among patchily distributed OTUs, we identified groups of OTUs correlated with common ecological drivers. For instance, a group of OTUs positively correlated with recent copepod feeding served to differentiate largely active growing copepods from those entering diapause. Together, our results underscore the power of individual-level sampling for understanding host-microbiome relationships.

Effects of ocean acidification on copepods

Ocean acidification (OA) leads to significant changes in seawater carbon chemistry, broadly affects marine organisms, and considered as a global threat to the fitness of marine ecosystems. Due to the crucial role of copepods in marine food webs of transferring energy from primary producers to higher trophic levels, numerous studies have been conducted to examine the impacts of OA on biological traits of copepods such as growth and reproduction. Under OA stress, the copepods demonstrated species-specific and stage-dependent responses. Notably, different populations of the same copepod species demonstrated different sensitivities to the increased pCO₂. In copepods, the deleterious effects of OA are also reinforced by other naturally occurring co-stressors (e.g., thermal stress, food deprivation, and metal pollution). Given that most OA stress studies have focused on the effects of short-term exposure (shorter than a single generation), experiments using adults might have underestimated the damaging effects of OA and the long-term multigenerational exposure to multiple stressors (e.g., increased pCO₂ and food shortage) will be required. Particularly, omics-based technologies (e.g., genomics, proteomics, and metabolomics) will be helpful to better understand the underlying processes behind biological responses (e.g., survival, development, and offspring production) at the mechanistic level which will improve our predictions of the responses of copepods to climate change stressors including OA.

How Do Marine Pelagic Species Respond to Climate Change? Theories and Observations

In this review, we show how climate affects species, communities, and ecosystems, and why many responses from the species to the biome level originate from the interaction between the species' ecological niche and changes in the environmental regime in both space and time. We describe a theory that allows us to understand and predict how marine species react to climate-induced changes in ecological conditions, how communities form and are reconfigured, and so how biodiversity is arranged and may respond to climate change. Our study shows that the responses of species to climate change are therefore intelligible-that is, they have a strong deterministic component and can be predicted.

Biogeographic responses of the copepod Calanus glacialis to a changing Arctic marine environment

Dramatic changes have occurred in the Arctic Ocean over the past few decades, especially in terms of sea ice loss and ocean warming. Those environmental changes may modify the planktonic ecosystem with changes from lower to upper trophic levels. This study aimed to understand how the biogeographic distribution of a crucial endemic copepod species, Calanus glacialis, may respond to both abiotic (ocean temperature) and biotic (phytoplankton prey) drivers. A copepod individual-based model coupled to an ice-ocean-biogeochemical model was utilized to simulate temperature- and food-dependent life cycle development of C. glacialis annually from 1980 to 2014. Over the 35-year study period, the northern boundaries of modeled diapausing C. glacialis expanded poleward and the annual success rates of C. glacialis individuals attaining diapause in a circumpolar transition zone increased substantially. Those patterns could be explained by a lengthening growth season (during which time food is ample) and shortening critical development time (the period from the first feeding stage N3 to the diapausing stage C4). The biogeographic changes were further linked to large-scale oceanic processes, particularly diminishing sea ice cover, upper ocean warming, and increasing and prolonging food availability, which could have potential consequences to the entire Arctic shelf/slope marine ecosystems.

De novo transcriptome assembly of the calanoid copepod Neocalanus flemingeri: A new resource for emergence from diapause

Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N. flemingeri. Since diapause is a developmental program, its progress can be tracked using through global gene expression. Thus, a reference transcriptome was developed as a first step towards physiological profiling of diapausing females using high-throughput Illumina sequencing. The de novo transcriptome, the first for this species was designed to investigate the diapause period. RNA-Seq reads were obtained for dormant to reproductive N. flemingeri females. A high quality de novo transcriptome was obtained by first assembling reads from each individual using Trinity software followed by clustering with CAP3 Assembly Program. This assembly consisted of 140,841transcripts (contigs). Bench-marking universal single-copy orthologs analysis identified 85% of core eukaryotic genes, with 79% predicted to be complete. Comparison with other calanoid transcriptomes confirmed its quality and degree of completeness. Trinity assembly of reads originating from multiple individuals led to fragmentation. Thus, the workflow applied here differed from the one recommended by Trinity, but was required to obtain a good assembly.