Genomic architecture constrains macromolecular allocation in dinoflagellates.

Dinoflagellate genomes have a unique architecture that may constrain their physiological and biochemical responsiveness to environmental stressors. Here we quantified how nitrogen (N) starvation influenced macromolecular allocation and C:N:P of three photosynthetic marine dinoflagellates, representing different taxonomic classes and genome sizes. Dinoflagellates respond to nitrogen starvation by decreasing cellular nitrogen, protein and RNA content, but unlike many other eukaryotic phytoplankton examined RNA:protein is invariant. Additionally, 2 of the 3 species exhibit increases in cellular phosphorus and very little change in cellular carbon with N-starvation. As a consequence, N starvation induces moderate increases in C:N, but extreme decreases in N:P and C:P, relative to diatoms. Dinoflagellate DNA content relative to total C, N and P is much higher than similar sized diatoms, but similar to very small photosynthetic picoeukaryotes such as Ostreococcus. In aggregate these results indicate the accumulation of phosphate stores may be an important strategy employed by dinoflagellates to meet P requirements associated with the maintenance and replication of their large genomes.

Common environmental stress responses in a model marine diatom.

Marine planktonic diatoms are among the most important contributors to phytoplankton blooms and marine net primary production. Their ecological success has been attributed to their ability to rapidly respond to changing environmental conditions. Here, we report common molecular mechanisms used by the model marine diatom Thalassiosira pseudonana to respond to 10 diverse environmental stressors using RNA-Seq analysis. We identify a specific subset of 1076 genes that are differentially expressed in response to stressors that induce an imbalance between energy or resource supply and metabolic capacity, which we termed the diatom environmental stress response (d-ESR). The d-ESR is primarily composed of genes that maintain proteome homeostasis and primary metabolism. Photosynthesis is strongly regulated in response to environmental stressors but chloroplast-encoded genes were predominantly upregulated while the nuclear-encoded genes were mostly downregulated in response to low light and high temperature. In aggregate, these results provide insight into the molecular mechanisms used by diatoms to respond to a range of environmental perturbations and the unique role of the chloroplast in managing environmental stress in diatoms. This study facilitates our understanding of the molecular mechanisms underpinning the ecological success of diatoms in the ocean.

Elemental stoichiometry of the key calcifying marine phytoplankton Emiliania huxleyi under ocean climate change: A meta-analysis.

The elemental composition of marine microorganisms (their C:N:P ratio, or stoichiometry) is central to understanding the biotic and biogeochemical processes underlying key marine ecosystem functions. Phytoplankton C:N:P is species specific and flexible to changing environmental conditions. However, bulk or fixed phytoplankton stoichiometry is usually assumed in biogeochemical and ecological models because more realistic, environmentally responsive C:N:P ratios have yet to be defined for key functional groups. Here, a comprehensive meta-analysis of experimental laboratory data reveals the variable C:N:P stoichiometry of Emiliania huxleyi, a globally significant calcifying phytoplankton species. Mean C:N:P of E. huxleyi is 124C:16N:1P under control conditions (i.e. growth not limited by one or more environmental stressors) and shows a range of responses to changes in nutrient and light availability, temperature and pCO2 . Macronutrient limitation caused strong shifts in stoichiometry, increasing N:P and C:P under P deficiency (by 305% and 493% respectively) and doubling C:N under N deficiency. Responses to light, temperature and pCO2 were mixed but typically shifted cellular elemental content and C:N:P stoichiometry by ca. 30% or less. Besides these independent effects, the interactive effects of multiple environmental changes on E. huxleyi stoichiometry under future ocean conditions could be additive, synergistic or antagonistic. To synthesise our meta-analysis results, we explored how the cellular elemental content and C:N:P stoichiometry of E. huxleyi may respond to two hypothetical future ocean scenarios (increased temperature, irradiance and pCO2 combined with either N deficiency or P deficiency) if an additive effect is assumed. Both future scenarios indicate decreased calcification (which is predominantly sensitive to elevated pCO2 ), increased C:N, and up to fourfold shifts in C:P and N:P. Our results strongly suggest that climate change will significantly alter the role of E. huxleyi (and potentially other calcifying phytoplankton species) in marine biogeochemical processes.

Density regulation amplifies environmentally induced population fluctuations.

Background: Density-dependent regulation is ubiquitous in population dynamics, and its potential interaction with environmental stochasticity complicates the characterization of the random component of population dynamics. Yet, this issue has not received attention commensurate with its relevance for descriptive and predictive modeling of population dynamics. Here we use a Bayesian modeling approach to investigate the contribution of density regulation to population variability in stochastic environments. Methods: We analytically derive a formula linking the stationary variance of population abundance/density under Gompertz regulation in a stochastic environment with constant variance to the environmental variance and the strength of density feedback, to investigate whether and how density regulation affects the stationary variance. We examine through simulations whether the relationship between stationary variance and density regulation inferred analytically under the Gompertz model carries over to the Ricker model, widely used in population dynamics modeling. Results: The analytical decomposition of the stationary variance under stochastic Gompertz dynamics implies higher variability for strongly regulated populations. Simulation results demonstrate that the pattern of increasing population variability with increasing density feedback found under the Gompertz model holds for the Ricker model as well, and is expected to be a general phenomenon with stochastic population models. We also analytically established and empirically validated that the square of the autoregressive parameter of the Gompertz model in AR(1) form represents the proportion of stationary variance due to density dependence. Discussion: Our results suggest that neither environmental stochasticity nor density regulation can alone explain the patterns of population variability in stochastic environments, as these two components of temporal variation interact, with a tendency for density regulation to amplify the magnitude of environmentally induced population fluctuations. This finding has far-reaching implications for population viability. It implies that intense intra-specific resource competition increases the risk of environment-driven population collapse at high density, making opportune harvesting a sensible practice for improving the resistance of managed populations such as fish stocks to environmental perturbations. The separation of density-dependent and density-independent processes will help improve population dynamics modeling, while providing a basis for evaluating the relative importance of these two categories of processes that remains a topic of long-standing controversy among ecologists.

Conservation and architecture of housekeeping genes in the model marine diatom Thalassiosira pseudonana.

Housekeeping genes (HKGs) are constitutively expressed with low variation across tissues/conditions. They are thought to be highly conserved and fundamental to cellular maintenance, with distinctive genomic features. Here, we identify 1505 HKGs in the unicellular marine diatom Thalassiosira pseudonana based on an RNA-seq analysis of 232 samples taken under 12 experimental conditions over 0-72 h. We identify promising internal reference genes (IRGs) for T. pseudonana from the most stably expressed HKGs. A comparative analysis indicates < 18% of HKGs in T. pseudonana have orthologs in other eukaryotes, including other diatom species. Contrary to work on human tissues, T. pseudonana HKGs are longer than non-HKGs, due to elongated introns. More ancient HKGs tend to be shorter than more recent HKGs, and expression levels of HKGs decrease more rapidly with gene length relative to non-HKGs. Our results indicate that HKGs are highly variable across the tree of life and thus unlikely to be universally fundamental for cellular maintenance. We hypothesize that the distinct genomic features of HKGs of T. pseudonana may be a consequence of selection pressures associated with high expression and low variance across conditions.

Contrasting transcriptomic responses of a microbial eukaryotic community to oil and dispersant.

Dispersants can aid dispersion and biodegradation of oil in seawater, but the wider ecotoxicological effects of oil and dispersant to the base of marine food webs is unclear. Here we apply a metatranscriptomic approach to identify molecular responses of a natural marine microbial eukaryotic community to oil and chemically dispersed oil. Oil exposure stimulated the upregulation of ketogenesis in the eukaryotic community, which may alleviate carbon- and energy-limitation and reduce oxidative stress. In contrast, a chemically dispersed oil treatment stimulated eukaryotic genes and pathways consistent with nitrogen and oxygen depletion. These results suggest that the addition of dispersant may elevate bacterial biodegradation of crude oil, indirectly increasing competition for nitrogen between prokaryotic and eukaryotic communities as oxygen consumption induces bacterial anaerobic respiration and denitrification. Eukaryotic microbial communities may mitigate some of the negative effects of oil exposure such as reduced photosynthesis and elevated oxidative stress, through ketosis, but the addition of dispersant to the oil fundamentally alters the environmental and ecological conditions and therefore the biochemical response of the eukaryotic community.

Telerehabilitation Using Fitness Application in Patients with Severe Cystic Fibrosis Awaiting Lung Transplant: A Pilot Study.

PURPOSE: The purpose of this study was to pilot a home-based pulmonary rehabilitation (PR) program administered via a telemedicine approach using a combination of fitness application and self-selected activity in lung transplant candidates with cystic fibrosis (CF). METHODS: We recruited adult patients with CF. The main outcome was adherence, measured by number of sessions completed in 12 weeks. Secondary outcomes were adverse events, six-minute walk distance (6MWD), and dyspnea. Participants were provided a personalized exercise program and equipment including a fitness application that provided exercise videos, recorded exercise time, and corresponding heart rate. We reviewed data daily and provided text messages with feedback. We compared our study outcomes to a retrospective data set of CF patients who participated in a 24-session outpatient hospital-based PR program. Data presented as mean ± standard deviation. RESULTS: Eleven patients participated in the home PR program, 45% female, age 33 ± 7 years, FEV1 27 ± 5% predicted. Sessions completed were 19 ± 12 home-based PR vs. 9 ± 4 hospital-based PR, p = .03. Fifty percent of the home-based group completed ≥24 sessions in 12 weeks versus 0% of the hospital-based patients (p = .03). There were no adverse events during exercise. Completers of the home-based program demonstrated a clinically meaningful lower decline in 6 MWD than noncompleters (6MWD -7 ± 15 vs. -86 ± 108 meters). Only one participant performed a post 6 MWD in the hospital-based PR. CONCLUSION: Patients with severe CF demonstrated adherence to home PR delivered using fitness application and self-selected activity with no adverse events. This program style may be a viable solution for telerehabilitation in severe CF and is particularly relevant in the COVID era.

Dynamic Photophysiological Stress Response of a Model Diatom to Ten Environmental Stresses.

Stressful environmental conditions can induce many different acclimation mechanisms in marine phytoplankton, resulting in a range of changes in their photophysiology. Here we characterize the common photophysiological stress response of the model diatom Thalassiosira pseudonana to ten environmental stressors and identify diagnostic responses to particular stressors. We quantify the magnitude and temporal trajectory of physiological parameters including the functional absorption cross-section of PSII (σPSII ), quantum efficiency of PSII, non-photochemical quenching (NPQ), cell volume, Chl a, and carotenoid (Car) content in response to nutrient starvation (nitrogen (N), phosphorus (P), silicon (Si), and iron (Fe)), changes in temperature, irradiance, pH, and reactive oxygen species (ROS) over 5 time points (0, 2, 6, 24, 72 h). We find changes in conditions: temperature, irradiance, and ROS, often result in the most rapid changes in photophysiological parameters (<2 h), and in some cases are followed by recovery. In contrast, nutrient starvation (N, P, Si, Fe) often has slower (6-72 h) but ultimately larger magnitude effects on many photophysiological parameters. Diagnostic changes include large increases in cell volume under Si-starvation, very large increases in NPQ under P-starvation, and large decreases in the σPSII under high light. The ultimate goal of this analysis is to facilitate and enhance the interpretation of fluorescence data and our understanding of phytoplankton photophysiology from laboratory and field studies.

Anthropogenic climate change impacts on copepod trait biogeography.

Copepods are among the most abundant marine metazoans and form a key link between marine primary producers, higher trophic levels, and carbon sequestration pathways. Climate change is projected to change surface ocean temperature by up to 4°C in the North Atlantic with many associated changes including slowing of the overturning circulation, areas of regional freshening, and increased salinity and reductions in nutrients available in the euphotic zone over the next century. These changes will lead to a restructuring of phytoplankton and zooplankton communities with cascading effects throughout the food web. Here we employ observations of copepods, projected changes in ocean climate, and species distribution models to show how climate change may affect the distribution of copepod species in the North Atlantic. On average species move northeast at a rate of 14.1 km decade-1 . Species turnover in copepod communities will range from 5% to 75% with the highest turnover rates concentrated in regions of pronounced temperature increase and decrease. The changes in species range vary according to copepod traits with the largest effects found to occur in the cooling, freshening area in the subpolar North Atlantic south of Greenland and in an area of significant warming along the Scotian shelf. Large diapausing copepods (>2.5 mm) which are higher in lipids and a crucial food source for whales, may have an advantage in the cooling waters due to their life-history strategy that facilitates their survival in the arctic environment. Carnivorous copepods show a basin wide increase in species richness and show significant habitat area increases when their distribution moves poleward while herbivores see significant habitat area losses. The trait-specific effects highlight the complex consequences of climate change for the marine food web.

Memory and mutualism in species sustainability: A time-fractional Lotka-Volterra model with harvesting.

We first present a predator-prey model for two species and then extend the model to three species where the two predator species engage in mutualistic predation. Constant effort harvesting and the impact of by-catch issue are also incorporated. Necessary sufficient conditions for the existence and stability of positive equilibrium points are examined. It is shown that harvesting is sustainable, and the memory concept of the fractional derivative damps out oscillations in the population numbers so that the system as a whole settles on an equilibrium quicker than it would with integer time derivatives. Finally, some possible physical explanations are given for the obtained results. It is shown that the stability requires the memory concept in the model.

Photosynthetic adaptation to light availability shapes the ecological success of bloom-forming cyanobacterium Pseudanabaena to iron limitation.

The poorly understood filamentous cyanobacterium Pseudanabaena is commonly epiphytic on Microcystis colonies and their abundances are often highly correlated during blooms. The response and adaptation of Microcystis to iron limitation have been extensively studied, but the strategies Pseudanabaena uses to respond to iron limitation are largely unknown. Here, physiological responses to iron limitation were compared between one Pseudanabaena and two Microcystis strains grown under different light intensities. The results showed that low-intensity light exacerbated, but high-intensity light alleviated, the negative effect of iron limitation on Pseudanabaena growth relative to two Microcystis strains. It was found that robust light-harvesting and photosynthetic efficiency allowed adaptation of Pseudanabaena to low light availability relative to two Microcystis strains only during iron sufficiency. The results also indicated that a larger investment in the photosynthetic antenna probably contributed to light/iron co-limitation of Pseudanabaena relative to two Microcystis strains under both light and iron limitation. Furthermore, the lower antenna pigments/chlorophyll a ratio and photosynthetic efficiency, and higher nonphotochemical quenching and saturation irradiance provided Pseudanabaena photoadaptation and photoprotection advantages over the two Microcystis strains under the high-light condition. The lower investment in antenna pigments of Pseudanabaena than the two Microcystis strains under high-light intensity is likely an efficient strategy for both saving iron quotas and decreasing photosensitivity. Therefore, when compared with Microcystis, the high plasticity of antenna pigments, along with the excellent photoadaptation and photoprotection ability of Pseudanabaena, probably ensures its ecological success under iron limitation when light is sufficient.

A Bayesian Framework for Robust Quantitative Trait Locus Mapping and Outlier Detection.

We introduce a Bayesian framework for simultaneous feature selection and outlier detection in sparse high-dimensional regression models, with a focus on quantitative trait locus (QTL) mapping in experimental crosses. More specifically, we incorporate the robust mean shift outlier handling mechanism into the multiple QTL mapping regression model and apply LASSO regularization concurrently to the genetic effects and the mean-shift terms through the flexible extended Bayesian LASSO (EBL) prior structure, thereby combining QTL mapping and outlier detection into a single sparse model representation problem. The EBL priors on the mean-shift terms prevent outlying phenotypic values from distorting the genotype-phenotype association and allow their detection as cases with outstanding mean shift values following the LASSO shrinkage. Simulation results demonstrate the effectiveness of our new methodology at mapping QTLs in the presence of outlying phenotypic values and simultaneously identifying the potential outliers, while maintaining a comparable performance to the standard EBL on outlier-free data.

A ribosomal sequence-based oil sensitivity index for phytoplankton groups.

Species-level variability has made it difficult to determine the relative sensitivity of phytoplankton to oil and mixtures of oil and dispersant. Here we develop a phytoplankton group sensitivity index using ribosome sequence data that we apply to a mesocosm experiment in which a natural microbial community was exposed to oil and two oil-dispersant mixtures. The relative sensitivity of four phytoplankton taxonomic groups, diatoms, dinoflagellates, green algae, and Chrysophytes, was computed using the log of the ratio of the number of species that increase to the number that decrease in relative abundance in the treatment relative to the control. The index indicates that dinoflagellates are the most sensitive group to oil and oil-dispersant treatments while the Chrysophytes benefit under oil exposure compared to the other groups examined. The phytoplankton group sensitivity index can be generally applied to quantify and rank the relative sensitivity of diverse microbial groups to environmental conditions and pollutants.

Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure.

The Deepwater Horizon oil spill released millions of barrels of crude oil into the Gulf of Mexico, and saw widespread use of the chemical dispersant Corexit. We assessed the role of traits, such as cell size, cell wall, motility, and mixotrophy on the growth and photosynthetic response of 15 phytoplankton taxa to oil and Corexit. We collected growth and photosynthetic data on five algal cultures. These responses could be separated into resistant (Tetraselmis astigmatica, Ochromonas sp., Heterocapsa pygmaea) and sensitive (Micromonas pusilla, Prorocentrum minimum). We combined this data with 10 species previously studied and found that cell size is most important in determining the biomass response to oil, whereas motility/mixotrophy is more important in the dispersed oil. Our analysis accounted for a third of the variance observed, so further work is needed to identify other factors that contribute to oil resistance.

Lymphoscintigraphic Abnormalities Associated with Milroy Disease and Lymphedema-Distichiasis Syndrome.

Background: Primary lymphedema is genetically heterogeneous. Two of the most common forms of primary lymphedema are Milroy disease (MD) and lymphedema-distichiasis syndrome (LDS). This study aims to look further into the pathogenesis of the two conditions by analyzing the lymphoscintigram images from affected individuals to ascertain if it is a useful diagnostic tool. Methods and Results: The lymphoscintigrams of patients with MD and LDS were analyzed, comparing the images and transport parameters of the two genotypes against a control population. Lymphoscintigrams were available for 12 MD and 16 LDS patients (all genetically proven diagnoses). Eight of the 12 (67%) lymph scans performed on patients with MD demonstrated little or no uptake from the initial lymphatics and poor visualization of the inguinal lymph nodes. These changes were consistent with a "functional aplasia," that is, the lymphatic vessels were present but appeared to be ineffective in absorbing the interstitial fluid into the lymphatic system. In patients with LDS the lymphoscintigraphic appearances were different. In 12 of the 16 scans (75%), the lymph scans were highly suggestive of lymphatic collector reflux. Quantification revealed a significantly reduced uptake of tracer within the inguinal lymph nodes and a higher residual activity in the feet at 2 hours in MD compared with LDS and compared with controls. Conclusion: Lymphoscintigraphic imaging and quantification can be characteristic in specific genetic forms of primary lymphedema and may be useful as an additional tool for in-depth phenotyping, leading to a more accurate diagnosis and providing insight into the underlying mechanism of disease.

Correction: Nitrogen starvation induces distinct photosynthetic responses and recovery dynamics in diatoms and prasinophytes.

[This corrects the article DOI: 10.1371/journal.pone.0195705.].

The macromolecular composition of noncalcified marine macroalgae.

The macromolecular composition of macroalgae influences nutrient flow and food quality in aquatic ecosystems and the value of macroalgae species for human consumption, aquaculture, biofuels, and other applications. We used literature data (125 publications, 1,117 observations) and a hierarchal Bayesian statistical model to estimate the average macromolecular composition, protein, lipid, and carbohydrate of macroalgae as a whole and at the phylum level. Our focus was on marine, noncalcified macroalgae sampled from wild-grown populations in the field. We found that the median macromolecular composition is 9.98% protein, 2.7% lipid, 48.5% carbohydrate, and 31.8% ash as percent dry weight. We compared the median macromolecular content of macroalgae to microalgae and herbaceous plants and test for differences in macromolecular content across macroalgal phyla. Macroalgae were much more enriched in carbohydrate and minerals than the microalgae and lower in protein and lipid than many herbaceous plants. Rhodophyte macroalgae have significantly less lipid and more protein and the Ochrophyte macroalgae have significantly less protein than the average.

The Macromolecular Basis of Phytoplankton C:N:P Under Nitrogen Starvation.

Biogeochemical cycles in the ocean are strongly affected by the elemental stoichiometry (C:N:P) of phytoplankton, which largely reflects their macromolecular content. A greater understanding of how this macromolecular content varies among phytoplankton taxa and with resource limitation may strengthen physiological and biogeochemical modeling efforts. We determined the macromolecular basis (protein, carbohydrate, lipid, nucleic acids, pigments) of C:N:P in diatoms and prasinophytes, two globally important phytoplankton taxa, in response to N starvation. Despite their differing cell sizes and evolutionary histories, the relative decline in protein during N starvation was similar in all four species studied and largely determined variations in N content. The accumulation of carbohydrate and lipid dominated the increase in C content and C:N in all species during N starvation, but these processes differed greatly between diatoms and prasinophytes. Diatoms displayed far greater accumulation of carbohydrate with N starvation, possibly due to their greater cell size and storage capacity, resulting in larger increases in C content and C:N. In contrast, the prasinophytes had smaller increases in C and C:N that were largely driven by lipid accumulation. Variation in C:P and N:P was species-specific and mainly determined by residual P pools, which likely represent intracellular storage of inorganic P and accounted for the majority of cellular P in all species throughout N starvation. Our findings indicate that carbohydrate and lipid accumulation may play a key role in determining the environmental and taxonomic variability in phytoplankton C:N. This quantitative assessment of macromolecular and elemental content spanning several marine phytoplankton species can be used to develop physiological models for ecological and biogeochemical applications.

Molecular mechanisms of temperature acclimation and adaptation in marine diatoms.

Diatoms are important contributors to marine primary production and the ocean carbon cycle, yet the molecular mechanisms that regulate their acclimation and adaptation to temperature are poorly understood. Here we use a transcriptomic approach to investigate the molecular mechanisms associated with temperature acclimation and adaptation in closely related colder- and warmer-adapted diatom species. We find evidence that evolutionary changes in baseline gene expression, which we termed transcriptional investment or divestment, is a key mechanism used by diatoms to adapt to different growth temperatures. Invested and divested pathways indicate that the maintenance of protein processing machinery and membrane structure, important short-term physiological mechanisms used to respond to temperature changes, are key elements associated with adaptation to different growth temperatures. Our results also indicate that evolutionary changes in the transcriptional regulation of acetyl-CoA associated pathways, including lipid and branched chain amino acid metabolism, are used by diatoms to balance photosynthetic light capture and metabolism with changes in growth temperature. Transcriptional investment and divestment can provide a framework to identify mechanisms of acclimation and adaption to temperature.