Connecting active to passive fluorescence with photosynthesis: a method for evaluating remote sensing measurements of Chl fluorescence

Recent advances in the retrieval of Chl fluorescence from space using passive methods (solar-induced Chl fluorescence, SIF) promise improved mapping of plant photosynthesis globally. However, unresolved issues related to the spatial, spectral, and temporal dynamics of vegetation fluorescence complicate our ability to interpret SIF measurements. We developed an instrument to measure leaf-level gas exchange simultaneously with pulse-amplitude modulation (PAM) and spectrally resolved fluorescence over the same field of view – allowing us to investigate the relationships between active and passive fluorescence with photosynthesis. Strongly correlated, slope-dependent relationships were observed between measured spectra across all wavelengths (Fλ, 670–850 nm) and PAM fluorescence parameters under a range of actinic light intensities (steady-state fluorescence yields, Ft) and saturation pulses (maximal fluorescence yields, Fm). Our results suggest that this method can accurately reproduce the full Chl emission spectra – capturing the spectral dynamics associated with changes in the yields of fluorescence, photochemical (ΦPSII), and nonphotochemical quenching (NPQ). We discuss how this method may establish a link between photosynthetic capacity and the mechanistic drivers of wavelength-specific fluorescence emission during changes in environmental conditions (light, temperature, humidity). Our emphasis is on future research directions linking spectral fluorescence to photosynthesis, ΦPSII, and NPQ

Disentangling Changes in the Spectral Shape of Chlorophyll Fluorescence : Implications for Remote Sensing of Photosynthesis

Novel satellite measurements of solar-induced chlorophyll fluorescence (SIF) can improve our understanding of global photosynthesis; however, little is known about how to interpret the controls on its spectral variability. To address this, we disentangle simultaneous drivers of fluorescence spectra by coupling active and passive fluorescence measurements with photosynthesis. We show empirical and mechanistic evidence for where, why, and to what extent leaf fluorescence spectra change. Three distinct components explain more than 95% of the variance in leaf fluorescence spectra under both steady-state and changing illumination conditions. A single spectral shape of fluorescence explains 84% of the variance across a wide range of species. The magnitude of this shape responds to absorbed light and photosynthetic up/down regulation; meanwhile, chlorophyll concentration and nonphotochemical quenching control 9% and 3% of the remaining spectral variance, respectively. The spectral shape of fluorescence is remarkably stable where most current satellite retrievals occur (far-red, >740nm), and dynamic downregulation of photosynthesis reduces fluorescence magnitude similarly across the 670- to 850-nm range. We conduct an exploratory analysis of hourly red and far-red canopy SIF in soybean, which shows a subtle change in red:far-red fluorescence coincident with photosynthetic downregulation but is overshadowed by longer-term changes in canopy chlorophyll and structure. Based on our leaf and canopy analysis, caution should be taken when attributing large changes in the spectral shape of remotely sensed SIF to plant stress, particularly if data acquisition is temporally sparse. Ultimately, changes in SIF magnitude at wavelengths greater than 740 nm alone may prove sufficient for tracking photosynthetic dynamics. Plain Language Summary Satellite remote sensing provides a global picture of photosynthetic activity-allowing us to see when, where, and how much CO2 plants are assimilating. To do this, satellites measure a small emission of energy from the plants called chlorophyll fluorescence. However, this measurement is typically made across a narrow wavelength range, while the emission spectrum (650-850 nm) is quite dynamic. We show where, why, and to what extent leaf fluorescence spectra change across a diverse range of species and conditions, ultimately informing canopy remote sensing measurements. Results suggest that wavelengths currently used by satellites are stable enough to track the downregulation of photosynthesis resulting from stress, while spectral shape changes respond more strongly to dynamics in canopy structure and chlorophyll concentration.Peer reviewe

Genetic diversity fuels gene discovery for tobacco and alcohol use

Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury(1-4). These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries(5). Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.Peer reviewe

Widespread deoxygenation of temperate lakes

The concentration of dissolved oxygen in aquatic systems helps to regulate biodiversity, nutrient biogeochemistry, greenhouse gas emissions, and the quality of drinking water. The long-term declines in dissolved oxygen concentrations in coastal and ocean waters have been linked to climate warming and human activity, but little is known about the changes in dissolved oxygen concentrations in lakes. Although the solubility of dissolved oxygen decreases with increasing water temperatures, long-term lake trajectories are difficult to predict. Oxygen losses in warming lakes may be amplified by enhanced decomposition and stronger thermal stratification8,9 or oxygen may increase as a result of enhanced primary production. Here we analyse a combined total of 45,148 dissolved oxygen and temperature profiles and calculate trends for 393 temperate lakes that span 1941 to 2017. We find that a decline in dissolved oxygen is widespread in surface and deep-water habitats. The decline in surface waters is primarily associated with reduced solubility under warmer water temperatures, although dissolved oxygen in surface waters increased in a subset of highly productive warming lakes, probably owing to increasing production of phytoplankton. By contrast, the decline in deep waters is associated with stronger thermal stratification and loss of water clarity, but not with changes in gas solubility. Our results suggest that climate change and declining water clarity have altered the physical and chemical environment of lakes. Declines in dissolved oxygen in freshwater are 2.75 to 9.3 times greater than observed in the world’s oceans and could threaten essential lake ecosystem services

Water uptake by older roots: evidence from desert succulents.

Abstract. Desert succulents are renowned for their rapid recovery of shoot function after periods of drought as a result of shoot succulence, root-shoot interactions, and key root properties. Near the base of the shoot, the proximal (generally older) roots appear to play a major role in the rapid uptake and delivery of water, especially after a period of soil drying when the rest of the root system has a lower hydraulic conductance. In all of the cacti, agaves, and yuccas examined to date, hydraulic conductance for the proximal root zone is unexpectedly high. Substantial water uptake by older roots of cacti is associated with much higher axial (xylem) hydraulic conductance in proximal than in distal root regions. For agaves and yuccas, proximal roots have other anatomical and physiological traits that enhance water uptake near the shoot base. Despite suberization (waxiness) of external root tissues in the proximal region, internal cell layers appear more characteristic of young root regions with living cortical cells and a high proportion of unsuberized passage cells in the endodermis. Both features may be related to the existence of a contractile root zone possessed by all members of the Agavaceae surveyed to date. Passage cells in the endodermis and aquaporins (protein water channels) in the metabolically active cortex expedite radial water transport. The radial swelling that accompanies longitudinal root contraction may also help maintain rootto-soil contact that would otherwise be diminished in dry soil. Modifications that increase axial and radial hydraulic conductance in the proximal root region suggest that water uptake by older roots is critical to the success of desert succulents

Hydraulic Conductance and Mercury-Sensitive Water Transport for Roots of Opuntia acanthocarpa in Relation to Soil Drying and Rewetting

Drought-induced changes in root hydraulic conductance (L(P)) and mercury-sensitive water transport were examined for distal (immature) and mid-root (mature) regions of Opuntia acanthocarpa. During 45 d of soil drying, L(P) decreased by about 67% for distal and mid-root regions. After 8 d in rewetted soil, L(P) recovered to 60% of its initial value for both regions. Axial xylem hydraulic conductivity was only a minor limiter of L(P). Under wet conditions, HgCl(2) (50 μm), which is known to block membrane water-transport channels (aquaporins), decreased L(P) and the radial hydraulic conductance for the stele (L(R, S)) of the distal root region by 32% and 41%, respectively; both L(P) and L(R, S) recovered fully after transfer to 2-mercaptoethanol (10 mm). In contrast, HgCl(2) did not inhibit L(P) of the mid-root region under wet conditions, although it reduced L(R, S) by 41%. Under dry conditions, neither L(P) nor L(R, S) of the two root regions was inhibited by HgCl(2). After 8 d of rewetting, HgCl(2) decreased L(P) and L(R, S) of the distal region by 23% and 32%, respectively, but L(P) and L(R, S) of the mid-root region were unaltered. Changes in putative aquaporin activity accounted for about 38% of the reduction in L(P) in drying soil and for 61% of its recovery for the distal region 8 d after rewetting. In the stele, changes in aquaporin activity accounted for about 74% of the variable L(R, S) during drought and after rewetting. Thus, aquaporins are important for regulating water movement for roots of O. acanthocarpa

Analysis of a hybrid numerical method – decomposing leaf hydraulic conductance

We describe a hybrid numerical method to solve a boundary value problem where an unknown parameter of the model is chosen to satisfy an additional boundary condition. After the solution of the differential equation is approximated using a one-step method, a secant method is used to update the value of the unknown parameter. The model is a generalization of a model first used to describe water flow through roots, which was later used to describe water flow through the tank bromeliad Guzmania lingulata. In both cases, identification of the unknown parameter represents the decomposition of overall plant conductance into components in the radial and axial directions. We describe convergence of the one-step and secant portions of the method in a base case corresponding to previous applications of the model and in an intermediate case corresponding to a first approximation of the geometry of the leaf. We demonstrate that in the more general case, which better represents the geometry of G. lingulata, the one-step method also converges as expected. Finally, we discuss the implications of including a better description of the geometry of the leaf in context of radial conductance and show that our modeling of the leaf geometry increases the component of the overall leaf conductance in the radial direction by as much as 25%

Leaf Hydraulic Conductance for a Tank Bromeliad: Axial and Radial Pathways for Moving and Conserving Water

Epiphytic plants in the Bromeliaceae known as tank bromeliads essentially lack stems and absorptive roots and instead take up water from reservoirs formed by their overlapping leaf bases. For such plants, leaf hydraulic conductance is plant hydraulic conductance. Their simple strap-shaped leaves and parallel venation make them suitable for modeling leaf hydraulic conductance based on vasculature and other anatomical and morphological traits. Plants of the tank bromeliad Guzmania lingulata were investigated in a lowland tropical forest in Costa Rica and a shaded glasshouse in Los Angeles, CA, USA. Stomatal conductance to water vapor and leaf anatomical variables related to hydraulic conductance were measured for both groups. Tracheid diameters and numbers of vascular bundles (veins) were used with the Hagen–Poiseuille equation to calculate axial hydraulic conductance. Measurements of leaf hydraulic conductance using the evaporative flux method were also made for glasshouse plants. Values for axial conductance and leaf hydraulic conductance were used in a model based on leaky cable theory to estimate the conductance of the radial pathway from the vein to the leaf surface and to assess the relative contributions of both axial and radial pathways. In keeping with low stomatal conductance, low stomatal density, low vein density, and narrow tracheid diameters, leaf hydraulic conductance for G. lingulata was quite low in comparison with most other angiosperms. Using the predicted axial conductance in the leaky cable model, the radial resistance across the leaf mesophyll was predicted to predominate; lower, more realistic values of axial conductance resulted in predicted radial resistances that were closer to axial resistance in their impact on total leaf resistance. Tracer dyes suggested that water uptake through the tank region of the leaf was not limiting. Both dye movement and the leaky cable model indicated that the leaf blade of G. lingulata was structurally and hydraulically well-suited to conserve water