Ocean acidification and ammonium enrichment interact to stimulate a short-term spike in growth rate of a bloom forming macroalga

IntroductionThe coastal macroalgal genus, Ulva, is found worldwide and is considered a nuisance algal genus due to its propensity for forming vast blooms. The response of Ulva to ocean acidification (OA) is of concern, particularly with nutrient enrichment, as these combined drivers may enhance algal blooms because of increased availability of dissolved inorganic resources.MethodsWe determined how a suite of physiological parameters were affected by OA and ammonium (NH4+) enrichment in 22-day laboratory experiments to gain a mechanistic understanding of growth, nutrient assimilation, and photosynthetic processes. We predicted how physiological parameters change across a range of pCO2 and NH4+ scenarios to ascertain bloom potential under future climate change regimes.ResultsDuring the first five days of growth, there was a positive synergy between pCO2 and NH4+ enrichment, which could accelerate initiation of an Ulva bloom. After day 5, growth rates declined overall and there was no effect of pCO2, NH4+, nor their interaction. pCO2 and NH4+ acted synergistically to increase NO3- uptake rates, which may have contributed to increased growth in the first five days. Under the saturating photosynthetically active radiation (PAR) used in this experiment (500 μmol photon m-2 s-1), maximum photosynthetic rates were negatively affected by increased pCO2, which could be due to increased sensitivity to light when high CO2 reduces energy requirements for inorganic carbon acquisition. Activity of CCMs decreased under high pCO2 and high NH4+ conditions indicating that nutrients play a role in alleviating photodamage and regulating CCMs under high-light intensities.DiscussionThis study demonstrates that OA could play a role in initiating or enhancing Ulva blooms in a eutrophic environment and highlights the need for understanding the potential interactions among light, OA, and nutrient enrichment in regulating photosynthetic processes

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Predicting Effects of Ocean Acidification and Warming on Algae Lacking Carbon Concentrating Mechanisms.

Seaweeds that lack carbon-concentrating mechanisms are potentially inorganic carbon-limited under current air equilibrium conditions. To estimate effects of increased atmospheric carbon dioxide concentration and ocean acidification on photosynthetic rates, we modeled rates of photosynthesis in response to pCO2, temperature, and their interaction under limiting and saturating photon flux densities. We synthesized the available data for photosynthetic responses of red seaweeds lacking carbon-concentrating mechanisms to light and temperature. The model was parameterized with published data and known carbonate system dynamics. The model predicts that direction and magnitude of response to pCO2 and temperature, depend on photon flux density. At sub-saturating light intensities, photosynthetic rates are predicted to be low and respond positively to increasing pCO2, and negatively to increasing temperature. Consequently, pCO2 and temperature are predicted to interact antagonistically to influence photosynthetic rates at low PFD. The model predicts that pCO2 will have a much larger effect than temperature at sub-saturating light intensities. However, photosynthetic rates under low light will not increase proportionately as pCO2 in seawater continues to rise. In the range of light saturation (Ik), both CO2 and temperature have positive effects on photosynthetic rate and correspondingly strong predicted synergistic effects. At saturating light intensities, the response of photosynthetic rates to increasing pCO2 approaches linearity, but the model also predicts increased importance of thermal over pCO2 effects, with effects acting additively. Increasing boundary layer thickness decreased the effect of added pCO2 and, for very thick boundary layers, overwhelmed the effect of temperature on photosynthetic rates. The maximum photosynthetic rates of strictly CO2-using algae are low, so even large percentage increases in rates with climate change will not contribute much to changing primary production in the habitats where they commonly live

Seawater carbonate chemistry and growth rate of a bloom forming macroalga

Introduction: The coastal macroalgal genus, Ulva, is found worldwide and is considered a nuisance algal genus due to its propensity for forming vast blooms. The response of Ulva to ocean acidification (OA) is of concern, particularly with nutrient enrichment, as these combined drivers may enhance algal blooms because of increased availability of dissolved inorganic resources. Methods: We determined how a suite of physiological parameters were affected by OA and ammonium (NH4+) enrichment in 22-day laboratory experiments to gain a mechanistic understanding of growth, nutrient assimilation, and photosynthetic processes. We predicted how physiological parameters change across a range of pCO2 and NH4+ scenarios to ascertain bloom potential under future climate change regimes. Results: During the first five days of growth, there was a positive synergy between pCO2 and NH4+ enrichment, which could accelerate initiation of an Ulva bloom. After day 5, growth rates declined overall and there was no effect of pCO2, NH4+, nor their interaction. pCO2 and NH4+ acted synergistically to increase NO3– uptake rates, which may have contributed to increased growth in the first five days. Under the saturating photosynthetically active radiation (PAR) used in this experiment (500 μmol photon/m**2/s), maximum photosynthetic rates were negatively affected by increased pCO2, which could be due to increased sensitivity to light when high CO2 reduces energy requirements for inorganic carbon acquisition. Activity of CCMs decreased under high pCO2 and high NH4+ conditions indicating that nutrients play a role in alleviating photodamage and regulating CCMs under high-light intensities. Discussion: This study demonstrates that OA could play a role in initiating or enhancing Ulva blooms in a eutrophic environment and highlights the need for understanding the potential interactions among light, OA, and nutrient enrichment in regulating photosynthetic processes

Standardized partial regression coefficients ± standard errors for (A) linear and (B) quadratic components of the best-fit regression model using AICc.

<p>Coefficients for temperature (open columns), CO₂ (filled columns), and the temperature*CO₂ interaction (stippled columns) are plotted for each of six light intensities ranging from 10 to 400 μmol photons · m^-2 · s^-1.</p

Discrimination against ¹³C by a model CO₂-using red alga as a function of light intensity.

<p>Solid line represents maximum discrimination expected at a given light intensity as a result of a minimal diffusive boundary layer. Increased diffusion path in a thicker boundary layer shifts the discrimination curve down (gray arrow). Note: X-axis scale is logarithmic.</p

Percentage increase in modeled rates of net photosynthesis, relative to rates at 380 μatm, as a function <i>p</i>CO₂ (μatm) for seaweeds in 5° (filled circles), 10° (open circles), 15° (squares), 20° (diamonds), 25° (triangles), or 30°C (pluses) seawater at representative sub-saturating (35 μmol photons · m^-2 · s^-1, top plot), or saturating (100 μmol photons · m^-2 · s^-1, bottom plot) light intensities.

<p>Percentage increase in modeled rates of net photosynthesis, relative to rates at 380 μatm, as a function <i>p</i>CO₂ (μatm) for seaweeds in 5° (filled circles), 10° (open circles), 15° (squares), 20° (diamonds), 25° (triangles), or 30°C (pluses) seawater at representative sub-saturating (35 μmol photons · m^-2 · s^-1, top plot), or saturating (100 μmol photons · m^-2 · s^-1, bottom plot) light intensities.</p

Modeled Q₁₀ response of net photosynthesis as a function <i>p</i>CO₂ (μatm) for seaweeds in seawater at 10° (circles), 15° (squares), 20° (diamonds), 25° (triangles), or 30°C (pluses) and representative sub-saturating (35 μmol photons · m^-2 · s^-1, top plot), or saturating (100 μmol photons · m^-2 · s^-1, bottom plot) photon flux densities.

<p>Modeled Q₁₀ response of net photosynthesis as a function <i>p</i>CO₂ (μatm) for seaweeds in seawater at 10° (circles), 15° (squares), 20° (diamonds), 25° (triangles), or 30°C (pluses) and representative sub-saturating (35 μmol photons · m^-2 · s^-1, top plot), or saturating (100 μmol photons · m^-2 · s^-1, bottom plot) photon flux densities.</p

Weighting coefficients of fractionation of ¹³C dissolved in CO₂ due to diffusion (<i>w</i>_αd) in seawater and carboxylation by RUBISCO (<i>w</i>_αc) as a function of light intensity (PPFD).

<p>PPFD measured in μmol photons m^-2 s^-1</p><p>Weighting coefficients of fractionation of ¹³C dissolved in CO₂ due to diffusion (<i>w</i>_αd) in seawater and carboxylation by RUBISCO (<i>w</i>_αc) as a function of light intensity (PPFD).</p

Predicted rates of net photosynthesis as a function of pathlength through the diffusive boundary layer at the thallus surface for (a.) subsaturating light (35 μmol photons · m^-2 · s^-1), or (b.) saturating light (400 μmol photons · m^-2 · s^-1) intensities.

<p>Lines represent power curves fit to predicted points at each combination of temperature (5 to 30°C at 5°C intervals) and <i>p</i>CO₂; purple, 380; blue, 460; green, 620; red, 780; black, 940 μatm)</p