Hypergraphs and centrality measures identifying key features in gene expression data.

Multidisciplinary approaches can significantly advance our understanding of complex systems. For instance, gene co-expression networks align prior knowledge of biological systems with studies in graph theory, emphasising pairwise gene to gene interactions. In this paper, we extend these ideas, promoting hypergraphs as an investigative tool for studying multi-way interactions in gene expression data. Additional freedoms are achieved by representing individual genes with hyperedges, and simultaneously testing each gene against many features/vertices. Further gene/hyperedge interactions can be captured and explored using the line graph representations, a technique that reduces the complexity of dense hypergraphs. Such an approach provides access to graph centrality measures, which identifies salient features within a data set. For instance dominant or hub-like hyperedges, leading to key knowledge on gene expression. The validity of this approach is established through the study of gene expression data for the plant species Senecio lautus and results will be interpreted within this biological setting.

Comparative experimental evolution reveals species-specific idiosyncrasies in marine phytoplankton adaptation to warming.

A number of experimental studies have demonstrated that phytoplankton can display rapid thermal adaptation in response to warmed environments. While these studies provide insight into the evolutionary responses of single species, they tend to employ different experimental techniques. Consequently, our ability to compare the potential for thermal adaptation across different, ecologically relevant, species remains limited. Here, we address this limitation by conducting simultaneous long-term warming experiments with the same experimental design on clonal isolates of three phylogenetically diverse species of marine phytoplankton; the cyanobacterium Synechococcus sp., the prasinophyte Ostreococcus tauri and the diatom Phaeodoactylum tricornutum. Over the same experimental time period, we observed differing levels of thermal adaptation in response to stressful supra-optimal temperatures. Synechococcus sp. displayed the greatest improvement in fitness (i.e., growth rate) and thermal tolerance (i.e., temperature limits of growth). Ostreococcus tauri was able to improve fitness and thermal tolerance, but to a lesser extent. Finally, Phaeodoactylum tricornutum showed no signs of adaptation. These findings could help us understand how the structure of phytoplankton communities may change in response to warming, and possible biogeochemical implications, as some species show relatively more rapid adaptive shifts in their thermal tolerance.

Calcifying Coccolithophore: An Evolutionary Advantage Against Extracellular Oxidative Damage.

The evolutionary advantages afforded by phytoplankton calcification remain enigmatic. In this work, fluoroelectrochemical experiments reveal that the presence of a CaCO3 shell of a naturally calcifying coccolithophore, Coccolithus braarudii, offers protection against extracellular oxidants as measured by the time required for the switch-off in their chlorophyll signal, compared to the deshelled equivalents, suggesting the shift toward calcification offers some advantages for survival in the surface of radical-rich seawater.

AI facilitated fluoro-electrochemical phytoplankton classification.

Marine phytoplankton is extremely diverse. Counting and characterising phytoplankton is essential for understanding climate change and ocean health not least since phytoplankton extensively biomineralize carbon dioxide whilst generating 50% of the planet's oxygen. We report the use of fluoro-electrochemical microscopy to distinguish different taxonomies of phytoplankton by the quenching of their chlorophyll-a fluorescence using chemical species oxidatively electrogenerated in situ in seawater. The rate of chlorophyll-a quenching of each cell is characteristic of the species-specific structural composition and cellular content. But with increasing diversity and extent of phytoplankton species under study, human interpretation and distinction of the resulting fluorescence transients becomes increasingly and prohibitively difficult. Thus, we further report a neural network to analyse these fluorescence transients, with an accuracy >95% classifying 29 phytoplankton strains to their taxonomic orders. This method transcends the state-of-the-art. The success of the fluoro-electrochemical microscopy combined with AI provides a novel, flexible and highly granular solution to phytoplankton classification and is adaptable for autonomous ocean monitoring.

The cellular response to ocean warming in Emiliania huxleyi.

Marine phytoplankton contribute substantially to the global flux of carbon from the atmosphere to the deep ocean. Sea surface temperatures will inevitably increase in line with global climate change, altering the performance of marine phytoplankton. Differing sensitivities of photosynthesis and respiration to temperature, will likely shift the strength of the future oceanic carbon sink. To further clarify the molecular mechanisms driving these alterations in phytoplankton function, shotgun proteomic analysis was carried out on the globally-occurring coccolithophore Emiliania huxleyi exposed to moderate- (23°C) and elevated- (28°C) warming. Compared to the control (17°C), growth of E. huxleyi increased under elevated temperatures, with higher rates recorded under moderate- relative to elevated- warming. Proteomic analysis revealed a significant modification of the E. huxleyi cellular proteome as temperatures increased: at lower temperature, ribosomal proteins and photosynthetic machinery appeared abundant, as rates of protein translation and photosynthetic performance are restricted by low temperatures. As temperatures increased, evidence of heat stress was observed in the photosystem, characterized by a relative down-regulation of the Photosystem II oxygen evolving complex and ATP synthase. Acclimation to elevated warming (28°C) revealed a substantial alteration to carbon metabolism. Here, E. huxleyi made use of the glyoxylate cycle and succinate metabolism to optimize carbon use, maintain growth and maximize ATP production in heat-damaged mitochondria, enabling cultures to maintain growth at levels significantly higher than those recorded in the control (17°C). Based on the metabolic changes observed, we can predict that warming may benefit photosynthetic carbon fixation by E. huxleyi in the sub-optimal to optimal thermal range. Past the thermal optima, increasing rates of respiration and costs of repair will likely constrain growth, causing a possible decline in the contribution of this species to the oceanic carbon sink depending on the evolvability of these temperature thresholds.

Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter.

Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is near-universally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores─single cells encrusted with biogenic calcite─to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a single-species coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell.

Rapid Opto-electrochemical Differentiation of Marine Phytoplankton.

The use of electro-generated oxidants in seawater facilitates the discrimination of different plankton groups via monitoring the decay in real time of their chlorophyll-a (chl-a) fluorescence signals following potentiostatic initiation of electrolysis in their vicinity (Yang M.Chem. Sci.2019, 10( (34), ), 7988-7993). In this paper, we explore the sensitivity of phytoplankton to different chemical species produced at various potentials in seawater. At low potentials, the oxidation of ca. millimolar bromide naturally present in seawater to hypobromous acid 'switches-off' the chl-a signal of individual Chlamydomonas concordia cells (green algae) located on the electrode surface within tens of seconds of the potential onset. At higher oxidative potentials, the oxidation of chloride and water produces oxidants (Cl2, OH, H2O2, etc.) that are also lethal to the plankton. To deconvolute the contributions to the response from the chemical identity of the oxidant and the amount of charge delivered to 'titrate' the individual living plankton using the loss of fluorescence as the 'end point', we introduce a ramped galvanostatic method. This approach enabled the controlled injection of charge applied to a bespoke electrochemical cell in which the plankton are immobilized on an electrode surface for rapid and sensitive measurement. It is shown that the number of moles (charge) of oxidants required to react leading to chl-a switch-off is independent of the chemical identity of the electro-generated oxidant(s) among hypobromous acid, chlorine, or water-derived oxidants. Comparative experiments between C. concordia and Emiliania huxleyi (where the latter are encapsulated by extracellular plates of calcium carbonate) show that significantly different amounts of absolute charge (moles of electro-generated oxidants) are required in each case to 'switch-off' the chl-a signal. The method provides the basis for a tool that could distinguish between different plankton cells within ca. 2 min including the setup time.

Phytoplankton biodiversity is more important for ecosystem functioning in highly variable thermal environments.

The 21st century has seen an acceleration of anthropogenic climate change and biodiversity loss, with both stressors deemed to affect ecosystem functioning. However, we know little about the interactive effects of both stressors and in particular about the interaction of increased climatic variability and biodiversity loss on ecosystem functioning. This should be remedied because larger climatic variability is one of the main features of climate change. Here, we demonstrated that temperature fluctuations led to changes in the importance of biodiversity for ecosystem functioning. We used microcosm communities of different phytoplankton species richness and exposed them to a constant, mild, and severe temperature-fluctuating environment. Wider temperature fluctuations led to steeper biodiversity-ecosystem functioning slopes, meaning that species loss had a stronger negative effect on ecosystem functioning in more fluctuating environments. For severe temperature fluctuations, the slope increased through time due to a decrease of the productivity of species-poor communities over time. We developed a theoretical competition model to better understand our experimental results and showed that larger differences in thermal tolerances across species led to steeper biodiversity-ecosystem functioning slopes. Species-rich communities maintained their ecosystem functioning with increased fluctuation as they contained species able to resist the thermally fluctuating environments, while this was on average not the case in species-poor communities. Our results highlight the importance of biodiversity for maintaining ecosystem functions and services in the context of increased climatic variability under climate change.

Opto-Electrochemical Dissolution Reveals Coccolith Calcium Carbonate Content.

Coccoliths are plates of biogenic calcium carbonate secreted by calcifying marine phytoplankton; annually these phytoplankton are responsible for exporting >1 billion tonnes (1015  g) of calcite to the deep ocean. Rapid and reliable methods for assessing the degree of calcification are technically challenging because the coccoliths are micron sized and contain picograms (pg) of calcite. Here we pioneer an opto-eletrochemical acid titration of individual coccoliths which allows 3D reconstruction of each individual coccolith via in situ optical imaging enabling direct inference of the coccolith mass. Coccolith mass ranging from 2 to 400 pg are reported herein, evidencing both inter- and intra-species variation over four different species. We foresee this scientific breakthrough, which is independent of knowledge regarding the species and calibration-free, will allow continuous monitoring and reporting of the degree of coccolith calcification in the changing marine environment.

Evolutionary temperature compensation of carbon fixation in marine phytoplankton.

The efficiency of carbon sequestration by the biological pump could decline in the coming decades because respiration tends to increase more with temperature than photosynthesis. Despite these differences in the short-term temperature sensitivities of photosynthesis and respiration, it remains unknown whether the long-term impacts of global warming on metabolic rates of phytoplankton can be modulated by evolutionary adaptation. We found that respiration was consistently more temperature dependent than photosynthesis across 18 diverse marine phytoplankton, resulting in universal declines in the rate of carbon fixation with short-term increases in temperature. Long-term experimental evolution under high temperature reversed the short-term stimulation of metabolic rates, resulting in increased rates of carbon fixation. Our findings suggest that thermal adaptation may therefore have an ameliorating impact on the efficiency of phytoplankton as primary mediators of the biological carbon pump.

Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment.

Rising sea surface temperatures are expected to lead to the loss of phytoplankton biodiversity. However, we currently understand very little about the interactions between warming, loss of phytoplankton diversity and its impact on the oceans' primary production. We experimentally manipulated the species richness of marine phytoplankton communities under a range of warming scenarios, and found that ecosystem production declined more abruptly with species loss in communities exposed to higher temperatures. Species contributing positively to ecosystem production in the warmed treatments were those that had the highest optimal temperatures for photosynthesis, implying that the synergistic impacts of warming and biodiversity loss on ecosystem functioning were mediated by thermal trait variability. As species were lost from the communities, the probability of taxa remaining that could tolerate warming diminished, resulting in abrupt declines in ecosystem production. Our results highlight the potential for synergistic effects of warming and biodiversity loss on marine primary production.

Global Posttrauma Symptoms: A Systematic Review of Qualitative Literature.

Exposure to potentially traumatic events is a global health problem, especially in low- and middle-income countries. Assessments for symptoms resulting from trauma exposure rely heavily on the Diagnostic and Statistical Manual of Mental Disorders, fifth edition (DSM-5) criteria for post-traumatic stress disorder (PTSD), which may not be relevant in all regions of the globe. We examined posttrauma symptoms that were not limited to Western constructs of mental health (i.e., PTSD). In a systematic review, we searched nine databases to identify posttrauma symptoms arising in qualitative literature published before July 17, 2017. A total of 17,938 records were identified and 392 met inclusion criteria. The 392 studies represented data on 400 study populations from 71 different nationalities/ethnicities. The presence and frequency of posttrauma symptoms were examined across all regions. Fisher's exact tests were also conducted to compare frequencies in posttrauma symptoms across region and gender. Based on a weighted analysis across regions, a list of global posttrauma symptoms (N = 85) was compiled into an item bank. We found that the majority of DSM-5 PTSD symptoms were mentioned across regions (with the exception of inability to recall specific aspects of the trauma and blame of self or others for the event). Across all regions, we also found a number of symptoms mentioned that were not part of PTSD and its associated features. Findings suggest that assessing posttrauma symptoms solely based on PTSD may be limiting to global populations. Research, policy, and practice implications are discussed.

Adaptation of phytoplankton to a decade of experimental warming linked to increased photosynthesis.

Phytoplankton photosynthesis is a critical flux in the carbon cycle, accounting for approximately 40% of the carbon dioxide fixed globally on an annual basis and fuelling the productivity of aquatic food webs. However, rapid evolutionary responses of phytoplankton to warming remain largely unexplored, particularly outside the laboratory, where multiple selection pressures can modify adaptation to environmental change. Here, we use a decade-long experiment in outdoor mesocosms to investigate mechanisms of adaptation to warming (+4 °C above ambient temperature) in the green alga Chlamydomonas reinhardtii, in naturally assembled communities. Isolates from warmed mesocosms had higher optimal growth temperatures than their counterparts from ambient treatments. Consequently, warm-adapted isolates were stronger competitors at elevated temperature and experienced a decline in competitive fitness in ambient conditions, indicating adaptation to local thermal regimes. Higher competitive fitness in the warmed isolates was linked to greater photosynthetic capacity and reduced susceptibility to photoinhibition. These findings suggest that adaptive responses to warming in phytoplankton could help to mitigate projected declines in aquatic net primary production by increasing rates of cellular net photosynthesis.