Partitioning net carbon dioxide fluxes into photosynthesis and respiration using neural networks

The eddy covariance (EC) technique is used to measure the net ecosystem exchange (NEE) of CO₂ between ecosystems and the atmosphere, offering a unique opportunity to study ecosystem responses to climate change. NEE is the difference between the total CO₂ release due to all respiration processes (RECO), and the gross carbon uptake by photosynthesis (GPP). These two gross CO₂ fluxes are derived from EC measurements by applying partitioning methods that rely on physiologically based functional relationships with a limited number of environmental drivers. However, the partitioning methods applied in the global FLUXNET network of EC observations do not account for the multiple co‐acting factors that modulate GPP and RECO flux dynamics. To overcome this limitation, we developed a hybrid data‐driven approach based on combined neural networks (NN_C‐part). NN_C‐part incorporates process knowledge by introducing a photosynthetic response based on the light‐use efficiency (LUE) concept, and uses a comprehensive dataset of soil and micrometeorological variables as fluxes drivers. We applied the method to 36 sites from the FLUXNET2015 dataset and found a high consistency in the results with those derived from other standard partitioning methods for both GPP (R² > .94) and RECO (R² > .8). High consistency was also found for (a) the diurnal and seasonal patterns of fluxes and (b) the ecosystem functional responses. NN_C‐part performed more realistic than the traditional methods for predicting additional patterns of gross CO₂ fluxes, such as: (a) the GPP response to VPD, (b) direct effects of air temperature on GPP dynamics, (c) hysteresis in the diel cycle of gross CO₂ fluxes, (d) the sensitivity of LUE to the diffuse to direct radiation ratio, and (e) the post rain respiration pulse after a long dry period. In conclusion, NN_C‐part is a valid data‐driven approach to provide GPP and RECO estimates and complementary to the existing partitioning methods.     

Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off

Rubisco assimilates CO₂ to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analyzed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO₂ and carboxylase turnover (∼21–37%), and between the Michaelis constants for CO₂ and O₂ (∼9–19%), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9%) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C₄ photosynthesis. Finally, we show that phylogenetic constraints have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all catalytic trade-offs.     

Metapopulation shift and survival of woodland birds under climate change: will species be able to track?

Climate change has been widely recognized as a key factor driving changes in species distributions. In this study we use a metapopulation model, with a window of suitable climate moving polewards, to explore population shifts and survival of woodland birds under different climate change scenarios and landscape configurations. Extinction vulnerability and expansion ability are predicted for the middle spotted woodpecker Dendrocopus medius and two alternative r‐K strategies under west European climate change scenarios of 1, 2 and 4°C temperature increase per century, corresponding to isotemperature velocities of ca 2, 4 and 8 km yr^?1. The simulated northward expansion of the bird's distribution is typically in the range of only 0–3 km yr^?1, in spite of 10–20 times larger maximum dispersal distances. This is too slow to track the climate change‐driven range contraction of 4 or 8 km yr^?1 in the south resulting in metapopulation extinction. Especially K‐selected (large‐bodied) species are vulnerable in the simulations. With a temperature increase of 4°C per century bird species go extinct within 104–178 yr. We present a simple approximation formula to predict the mean time to metapopulation extinction using 1) the rate of climate change, which determines the speed of range contraction in the south, 2) the size of the distribution range, which serves as a buffer against extinction, and 3) the northward expansion velocity, determined by species traits and landscape properties. Finally, our results indicate that the northward expansion rate is not constant. It will be initially lagged suggesting that recently observed expansion rates might be underestimations of future northward expansion rates.     

Influence of intravenously administered leptin on nitric oxide production, renal hemodynamics and renal function in the rat

We investigated the effect of leptin on systemic nitric oxide (NO) production, arterial pressure, renal hemodynamics and renal excretory function in the rat. Leptin (1 mg/kg) was injected intravenously and mean arterial pressure (MAP), heart rate (HR), renal blood flow (RBF) and renal cortical blood flow (RCBF), were measured for 210 min after injection. Urine was collected for seven consecutive 30-min periods and blood samples were withdrawn at 15, 45, 75, 105, 135, 165 and 195 min after leptin administration. Leptin had no effect on MAP, HR, RBF, RCBF and creatinine clearance, but increased urine output by 37.8% (0–30 min), 32.4% (31–60 min) and 27.0% (61–90 min), as well as urinary sodium excretion by 175.8% (0–30 min), 136.4% (31–60 min) and 124.2% (61–90 min). In contrast, leptin had no effect on potassium and phosphate excretion. Plasma concentration of NO metabolites, nitrites+nitrates (NO_x), increased following leptin injection at 15, 45, 75 and 105 min by 27.7%, 178.1%, 156.4% and 58.7%, respectively. Leptin increased urinary NO_x excretion by 241.6% (0–30 min), 552.6% (31–60 min), 430.7% (61–90 min) and 88.9% (91–120 min). This was accompanied by increase in plasma and urinary cyclic GMP. These data indicate that leptin stimulates systemic NO production but has no effect on arterial pressure and renal hemodynamics.     

Estuarine Microbial Food Web Patterns in a Lake Erie Coastal Wetland

Composition and distribution of planktonic protists were examined relative to microbial food web dynamics (growth, grazing, and nitrogen cycling rates) at the Old Woman Creek (OWC) National Estuarine Research Reserve during an episodic storm event in July 2003. More than 150 protistan taxa were identified based on morphology. Species richness and microbial biomass measured via microscopy and flow cytometry increased along a stream–lake (Lake Erie) transect and peaked at the confluence. Water column ammonium (NH₄⁺) uptake (0.06 to 1.82 M N h^–1) and regeneration (0.04 to 0.55 M N h^–1) rates, measured using ¹⁵NH₄⁺ isotope dilution, followed the same pattern. Large light/dark NH₄⁺ uptake differences were observed in the hypereutrophic OWC interior, but not at the phosphorus-limited Lake Erie site, reflecting the microbial community structural shift from net autotrophic to net heterotrophic. Despite this shift, microbial grazers (mostly choreotrich ciliates, taxon-specific growth rates up to 2.9 d^–1) controlled nanophytoplankton and bacteria at all sites by consuming 76 to 110% and 56 to 97% of their daily production, respectively, in dilution experiments. Overall, distribution patterns and dynamics of microbial communities in OWC resemble those in marine estuaries, where plankton productivity increases along the river–sea gradient and reaches its maximum at the confluence.     

Microbial ammonium cycling in the Mississippi River plume during the drought spring of 2000

Microbial potential uptake and regeneration rates of ammonium(NH₄⁺) were studied along a salinity gradient (salinities 0.2–34.4)in the Mississippi River plume during an extreme drought inspring 2000. Chlorophyll concentrations up to 30 µg L^–1were highest in the low- and mid-salinity regions (salinities8.5–28.2) and comparable to records of other years butextended over smaller areas than during periods of normal riverflow. Bacterial biomass (5.1–28.3 µg C L^–1)was at the low end of the range observed in normal flow years,decreased with distance from the river mouth and did not peakwith chlorophyll. Heterotrophic nanoflagellate abundance (1.4–4.0µg C L^–1) did not reflect phytoplankton and bacterialspatial distribution but peaked at 9.2 µg C L^–1at salinity 8.5. Microbial NH₄⁺ regeneration rates were estimatedby ¹⁵NH₄⁺ isotope dilution experiments for the whole microbialcommunity, under light and dark conditions, and for the <2µm bacterium-dominated size fraction. Microbial NH₄⁺ regenerationrates (0.018–0.124 µmol N L^–1 h^–1) werelow relative to previous reports and peaked at salinity 28.Total NH₄⁺ regeneration rates were higher than those in the<2 µm size fraction at only four stations, suggestingthat bacterial mineralization was a significant component ofNH₄⁺ recycling in some parts of the river plume. Higher NH₄⁺regeneration in whole-water samples versus <2 µm fractionsprovided evidence for microbial grazing in regions where chlorophylland regeneration rates peaked and at two full-salinity stations.     

Determinants for membrane association and permeabilization of the coxsackievirus 2B protein and the identification of the Golgi complex as the target organelle

The 2B protein of enterovirus is responsible for the alterations in the permeability of secretory membranes and the plasma membrane in infected cells. The structural requirements for the membrane association and the subcellular localization of this essential virus protein, however, have not been defined. Here, we provide evidence that the 2B protein is an integral membrane protein in vivo that is predominantly localized at the Golgi complex upon individual expression. Addition of organelle-specific targeting signals to the 2B protein revealed that the Golgi localization is an absolute prerequisite for the ability of the protein to modify plasma membrane permeability. Expression of deletion mutants and heterologous proteins containing specific domains of the 2B protein demonstrated that each of the two hydrophobic regions could mediate membrane binding individually. However, the presence of both hydrophobic regions was required for the correct membrane association, efficient Golgi targeting, and the membrane-permeabilizing activity of the 2B protein, suggesting that the two hydrophobic regions are cooperatively involved in the formation of a membrane-integral complex. The formation of membrane-integral pores by the 2B protein in the Golgi complex and the possible mechanism by which a Golgi-localized virus protein modifies plasma membrane permeability are discussed.     

Projected effects of Climate‐change‐induced flow alterations on stream macroinvertebrate abundances

Global change has the potential to affect river flow conditions which are fundamental determinants of physical habitats. Predictions of the effects of flow alterations on aquatic biota have mostly been assessed based on species ecological traits (e.g., current preferences), which are difficult to link to quantitative discharge data. Alternatively, we used empirically derived predictive relationships for species’ response to flow to assess the effect of flow alterations due to climate change in two contrasting central European river catchments. Predictive relationships were set up for 294 individual species based on (1) abundance data from 223 sampling sites in the Kinzig lower‐mountainous catchment and 67 sites in the Treene lowland catchment, and (2) flow conditions at these sites described by five flow metrics quantifying the duration, frequency, magnitude, timing and rate of flow events using present‐day gauging data. Species’ abundances were predicted for three periods: (1) baseline (1998–2017), (2) horizon 2050 (2046–2065) and (3) horizon 2090 (2080–2099) based on these empirical relationships and using high‐resolution modeled discharge data for the present and future climate conditions. We compared the differences in predicted abundances among periods for individual species at each site, where the percent change served as a proxy to assess the potential species responses to flow alterations. Climate change was predicted to most strongly affect the low‐flow conditions, leading to decreased abundances of species up to ?42%. Finally combining the response of all species over all metrics indicated increasing overall species assemblage responses in 98% of the studied river reaches in both projected horizons and were significantly larger in the lower‐mountainous Kinzig compared to the lowland Treene catchment. Such quantitative analyses of freshwater taxa responses to flow alterations provide valuable tools for predicting potential climate‐change impacts on species abundances and can be applied to any stressor, species, or region.     

Anion-sensitive ATPase activity and proton transport in isolated vacuoles of species of the CAM genus Kalanchoë

Vacuoles were isolated from leaves of Kalanchoë daigremontiana Hamet et Perrier de la Bathie, and the ionic sensitivity of the vacuolar ATPase was studied in vacuole homogenates desalted on Sephadex G-25. The ATPase activity was dependent on the presence of divalent cations (Mg²⁺≥ Mn²⁺≥ Ca²⁺, Co²⁺; Zn²⁺ had no effect). Mg²⁺-dependent ATPase activity was stimulated by anions (Cl^? > malate²⁺, HCO^?₃), with maximal stimulation at concentrations above 50 mM. Mg²⁺-Dependent activity was inhibited by NO^?₃ above 2 mM, but no saturation was observed up to 100 mM. No stimulation by K⁺ or Na⁺ was detected; stimulation by NH⁺₄ was abolished by 0.01% (w/v) Triton X-100, suggesting that the NH⁺₄ effect was due to the permeability of vacuolar membrane vesicles to NH₃. Trans-tonoplast electrical potentials (Δψ) and intra-vacuolar pH were measured with glass microelectrodes and antimony covered glass micro-pH-electrodes, respectively. Free vacuofes isolated from Kalanchoë tubiflora (Harv.) Hamet were slightly positive with respect to the suspension medium. This Δψ was insensitive to the protonophore FCCP and depolarized by about 4 mV on addition of 50 mM KCl, still remaining about +5 mV. Upon addition of 7 mM Mg-ATP, vacuoles showed an FCCP-sensitive increase of Δψ from +9.2 ± 2.8 (13) to +17.8 ± 3.7 (12) mV [given as x?± sd (n)] and an internal acidification from pH 5.4 ± 0.2 (11) to pH 4.3 ± 0.4 (12). Mg-ADP and ATP without Mg²⁺ had no effect on Δψ. It is concluded that the H4 pumping at the tonoplast is due to the functioning of the anion-sensitive vacuolar ATPase and that this is an essential part of the mechanism of nocturnal acid accumulation in CAM.