The many meanings of gross photosynthesis and their implication for photosynthesis research from leaf to globe

The effects of teleconnections on water and carbon fluxes in the two South America's largest biomes

Ecosystem services provided by terrestrial biomes, such as moisture recycling and carbon assimilation, are crucial components of the water, energy, and biogeochemical cycles. These biophysical processes are influenced by climate variability driven by distant ocean-atmosphere interactions, commonly referred to as teleconnections. This study aims to identify which teleconnections most significantly affect key biophysical processes in South America's two largest biomes: The Amazon and Cerrado. Using 20 years of monthly data on Precipitation (P), Evapotranspiration (ET), Gross Primary Productivity (GPP), and Ecosystem Water Use Efficiency (EWUE), alongside data from six teleconnections (Antarctic Oscillation - AAO, Atlantic Multidecadal Oscillation - AMO, Oceanic Niño Index - ONI, Atlantic Meridional Mode - AMM, North Atlantic Oscillation - NAO, and Pacific Decadal Oscillation - PDO), we developed a multivariate linear model to assess the relative importance of each teleconnection. Additionally, time-lagged Spearman correlations were used to explore relationships between biophysical variables and teleconnections. Our findings indicate that the AMO exerts the strongest influence across all studied variables. Furthermore, ONI and AMM significantly impact precipitation in the northern Amazon, with a 3-month lag in ONI showing positive correlations with ET and GPP. In contrast, a 3-month lag in AMO negatively influences GPP in the southern Amazon and Cerrado, though positive correlations with EWUE were observed in the same region. These insights highlight the complex and regionally varied impacts of teleconnections on South America's largest biomes.

Genome-wide comparative analysis of photosynthetic enzymatic genes provides novel insights into foxtail millet and other cereals

C4 crops have more efficient photosynthetic pathways that enable their higher photosynthetic capacities as well as nitrogen and water use efficiencies than C3 crops. Previous research has demonstrated that the genomes of C3 species include and express every gene needed for the C4 photosynthesis pathway. However, very little is known about the dynamics and evolutionary history of such genetic evolution in C4 plants. In this study, the genes encoding five key photosynthetic pathway enzymes in the genomes of C3 (rice), C4 (maize, sorghum, and foxtail millet), and CAM (pineapple) crops were identified and compared systematically. The numbers of genes in these photosynthetic enzymes were highest in the C4 crops like sorghum and foxtail millet, while only eight genes were identified in the CAM plant. However, 16 genes were identified in the C3 crop rice. Furthermore, we performed physical, chemical, gene structure and, cis-element analyses to obtain complete insights into these key genes. Tissue-specific expressions showed that most of the photosynthetic genes are expressed in the leaf tissues. Comparisons of the expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among the species, while the C4 gene copies in the C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that could affect C4 gene expressions and subcellular localization were found in the coding and promoter regions. Our research also highlights the variations in how different genes have evolved within the C4 photosynthetic pathway, and we confirmed that specific high expressions in the leaves and right distribution within the cells were crucial for the development of the C4 photosynthetic abilities. The findings of this study are expected to aid in understanding the evolutionary process of the C4 photosynthetic pathway in grasses as well as offer insights for modifying the C4 photosynthetic pathways in wheat, rice, and other significant C3 cereal crops.

Nitric Oxide Mitigates the Deleterious Effects Caused by Infection of Pseudomonas syringae pv. syringae and Modulates the Carbon Assimilation Process in Sweet Cherry under Water Stress

Bacterial canker is an important disease of sweet cherry plants mainly caused by Pseudomonas syringae pv. syringae (Pss). Water deficit profoundly impairs the yield of this crop. Nitric oxide (NO) is a molecule that plays an important role in the plant defense mechanisms. To evaluate the protection exerted by NO against Pss infection under normal or water-restricted conditions, sodium nitroprusside (SNP), a NO donor, was applied to sweet cherry plants cv. Lapins, before they were exposed to Pss infection under normal or water-restricted conditions throughout two seasons. Well-watered plants treated with exogenous NO presented a lower susceptibility to Pss. A lower susceptibility to Pss was also induced in plants by water stress and this effect was increased when water stress was accompanied by exogenous NO. The lower susceptibility to Pss induced either by exogenous NO or water stress was accompanied by a decrease in the internal bacterial population. In well-watered plants, exogenous NO increased the stomatal conductance and the net CO2 assimilation. In water-stressed plants, NO induced an increase in the leaf membranes stability and proline content, but not an increase in the CO2 assimilation or the stomatal conductance.

A Beginner's Guide to Eddy Covariance: Methodology and Its Applications to Photosynthesis

The eddy covariance technique, commonly applied using flux towers, enables the investigation of greenhouse gas (e.g., carbon dioxide, methane, nitrous oxide) and energy (latent and sensible heat) fluxes between the biosphere and the atmosphere. Through measuring carbon fluxes in particular, eddy covariance flux towers can give insight into how ecosystem scale photosynthesis (i.e., gross primary productivity) changes over time in response to climate and management. This chapter is designed to be a beginner's guide to understanding the eddy covariance method and how it can be applied in photosynthesis research. It introduces key concepts and assumptions that apply to the method, what materials are required to set up a flux tower, as well as practical advice for site installation, maintenance, data management, and postprocessing considerations. This chapter also includes examples of what can go wrong, with advice on how to correct these errors if they arise. This chapter has been crafted to help new users design, install, and manage the best towers to suit their research needs and includes additional resources throughout to further guide successful eddy covariance research activities.

Isotopic clumping in wood as a proxy for photorespiration in trees

Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO2]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups (R-O-CH3) in wood. Most methoxyl C-H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue 13CH2D correlates with temperature (18-28 °C) and atmospheric [CO2] (280-1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO2] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood.

Construction of a new LED chamber to measure net ecosystem exchange in low vegetation and validation study in grain crops

A vegetation canopy chamber system measures gas exchanges in the field between plants and the environment. Transparent closed chambers have generally been used to measure canopy fluxes in the field, depending on solar radiation as the light source for photosynthesis. However, measuring canopy fluxes in nature can be challenging due to fluctuations in solar radiation. Therefore, we constructed a novel transient-state closed-chamber system using light-emitting diodes (LEDs) as a light source to measure canopy-scale fluxes. The water-cooled chamber system used a 1600 Watt LED module to produce constant photosynthetically active radiation (PAR) and a CO₂ gas analyzer for concentration measurements. We used the LED chamber system to measure barley and wheat gas exchanges in the field to quantify CO₂ fluxes along a PAR gradient. This novel technology enables the determination of photosynthesis rates for various crops under diverse environmental conditions, in diverse ecosystems, and across long-term interannual changes, including those due to climate change.

Responses of Anabaena sp. PCC7120 to lindane: Physiological effects and differential expression of potential lin genes

Lindane (γ-HCH) is an organochlorine pesticide that causes huge environmental concerns worldwide due to its recalcitrance and toxicity. The use of the cyanobacterium Anabaena sp. PCC 7120 in aquatic lindane bioremediation has been suggested but information relative to this process is scarce. In the present work, data relative to the growth, pigment composition, photosynthetic/respiration rate, and oxidative stress response of Anabaena sp. PCC 7120 in the presence of lindane at its solubility limit in water are shown. In addition, lindane degradation experiments revealed almost a total disappearance of lindane in the supernatants of Anabaena sp. PCC 7120 culture after 6 days of incubation. The diminishing in lindane concentration was in concordance with an increase in the levels of trichlorobenzene inside the cells. Furthermore, to identify potential orthologs of the linA, linB, linC, linD, linE, and linR genes from Sphingomonas paucimobilis B90A in Anabaena sp. PCC 7120, a whole genome screening was performed allowing the identification of five putative lin orthologs (all1353 and all0193 putative orthologs of linB, all3836 putative orthologs of linC, and all0352 and alr0353 putative orthologs of linE and linR, respectively) which could be involved in the lindane degradation pathway. Differential expression analysis of these genes in the presence of lindane revealed strong upregulation of one of the potential lin genes of Anabaena sp. PCC 7120.

Climate-driven shifts in kelp forest composition reduce carbon sequestration potential

The potential contribution of kelp forests to blue carbon sinks is currently of great interest but interspecific variance has received no attention. In the temperate Northeast Atlantic, kelp forest composition is changing due to climate-driven poleward range shifts of cold temperate Laminaria digitata and Laminaria hyperborea and warm temperate Laminaria ochroleuca. To understand how this might affect the carbon sequestration potential (CSP) of this ecosystem, we quantified interspecific differences in carbon export and decomposition alongside changes in detrital photosynthesis and biochemistry. We found that while warm temperate kelp exports up to 71% more carbon per plant, it decomposes up to 155% faster than its boreal congeners. Elemental stoichiometry and polyphenolic content cannot fully explain faster carbon turnover, which may be attributable to contrasting tissue toughness or unknown biochemical and structural defenses. Faster decomposition causes the detrital photosynthetic apparatus of L. ochroleuca to be overwhelmed 20 days after export and lose integrity after 36 days, while detritus of cold temperate species maintains carbon assimilation. Depending on the photoenvironment, detrital photosynthesis could further exacerbate interspecific differences in decomposition via a potential positive feedback loop. Through compositional change such as the predicted prevalence of L. ochroleuca, ocean warming may therefore reduce the CSP of such temperate marine forests.

The Water Storage Function of Litters and Soil in Five Typical Plantations in the Northern and Southern Mountains of Lanzhou, Northwest China

Soil and water conservation is an important function of forest ecosystems; however, it remains unclear which forest type is best suited for water and soil conservation under the same site conditions. In order to clarify the soil and water conservation function of different plantations in the northern and southern mountains of Lanzhou city, we investigated several soil and water conservation function indicators (thickness and accumulation of litter, maximum water holding capacity and rate of litter, water holding capacity and water absorption rate of litter, soil infiltration rates, soil water content, soil bulk density, soil porosity, and soil water storage) of five plantation types (Platycladus orientalis plantations (Po), Robinia pseudoacacia plantations (Rp), Populus alba var. pyramidalis plantations (Pa), P. alba var. pyramidalis + R. pseudoacacia mixed plantations (Pa + Rp), and P. orientalis + R. pseudoacacia mixed plantations (Po + Rp)) and evaluated them using the gray correlation method. The results indicated the accumulation of litter varied from 13.50 to 47.01 t·hm−2 and increased in the order of Pa < Rp < Po < Po + Rp < Pa + Rp. The maximum water holding capacity of litter varied from 35.29 to 123.59 t·hm−2 and increased in the order of Pa < Rp < Po < Po + Rp < Pa + Rp. The soil physical properties (soil infiltration, porosity, and bulk density) of mixed plantations were better than those of pure plantations. The soil maximum water storage was significantly different among plantation types (p < 0.05), with an average varying from 3930.87 to 4307.45 t·hm−2, and was greater in mixed plantations than in pure plantations. Gray correlation analysis revealed that mixed plantations had the best conservation function of the five plantation types, followed by broad-leaved plantations and coniferous plantations. This suggests that the planting of mixed plantations dominated by Pa + Rp is therefore recommended in the future construction of plantations in the northern and southern mountains of Lanzhou to realize sustainable forest development.

Mathematical Modeling to Estimate Photosynthesis: A State of the Art

Photosynthesis is a process that indicates the productivity of crops. The estimation of this variable can be achieved through methods based on mathematical models. Mathematical models are usually classified as empirical, mechanistic, and hybrid. To mathematically model photosynthesis, it is essential to know: the input/output variables and their units; the modeling to be used based on its classification (empirical, mechanistic, or hybrid); existing measurement methods and their invasiveness; the validation shapes and the plant species required for experimentation. Until now, a collection of such information in a single reference has not been found in the literature, so the objective of this manuscript is to analyze the most relevant mathematical models for the photosynthesis estimation and discuss their formulation, complexity, validation, number of samples, units of the input/output variables, and invasiveness in the estimation method. According to the state of the art reviewed here, 67% of the photosynthesis measurement models are mechanistic, 13% are empirical and 20% hybrid. These models estimate gross photosynthesis, net photosynthesis, photosynthesis rate, biomass, or carbon assimilation. Therefore, this review provides an update on the state of research and mathematical modeling of photosynthesis.

The physiological basis for estimating photosynthesis from Chla fluorescence

Solar-induced Chl fluorescence (SIF) offers the potential to curb large uncertainties in the estimation of photosynthesis across biomes and climates, and at different spatiotemporal scales. However, it remains unclear how SIF should be used to mechanistically estimate photosynthesis. In this study, we built a quantitative framework for the estimation of photosynthesis, based on a mechanistic light reaction model with the Chla fluorescence of Photosystem II (SIFPSII ) as an input (MLR-SIF). Utilizing 29 C3 and C4 plant species that are representative of major plant biomes across the globe, we confirmed the validity of this framework at the leaf level. The MLR-SIF model is capable of accurately reproducing photosynthesis for all C3 and C4 species under diverse light, temperature, and CO2 conditions. We further tested the robustness of the MLR-SIF model using Monte Carlo simulations, and found that photosynthesis estimates were much less sensitive to parameter uncertainties relative to the conventional Farquhar, von Caemmerer, Berry (FvCB) model because of the additional independent information contained in SIFPSII . Once inferred from direct observables of SIF, SIFPSII provides 'parameter savings' to the MLR-SIF model, compared to the mechanistically equivalent FvCB model, and thus avoids the uncertainties arising as a result of imperfect model parameterization. Our findings set the stage for future efforts to employ SIF mechanistically to improve photosynthesis estimates across a variety of scales, functional groups, and environmental conditions.

Glyphosate at low doses changes the physiology and increases the productivity of common bean as affected by sowing seasons

Glyphosate applied at low doses can stimulate photosynthesis and yield. The objective of this study was to evaluate the application of low doses of glyphosate and sowing seasons in physiological characteristics and grain yield of common bean of early cycle. Two experiments were conducted in the field, the first in winter season and the second in wet season. The experimental design was a randomized complete block design, consisting of five and seven low doses of glyphosate and one period of application, with four replications. Glyphosate low dose of 108.0 g a.e. ha-1 impaired net CO2 assimilation rate, stomatal conductance, transpiration rate, instantaneous carboxylation efficiency, number of pods per plant, number of grains per plant and number of grains per pod. Glyphosate dose of 7.2 g a.e. ha-1 provided a 23% increase in grain yield in winter season, and the dose of 36.0 g a.e. ha-1 provided a 109% increase in grain yield in wet season. To our knowledge, this is the first report on effect of glyphosate at low doses and sowing season to obtain yield increases in common bean of early cycle.

Citrus photosynthesis and morphology acclimate to phloem-affecting huanglongbing disease at the leaf and shoot levels

Huanglongbing (HLB) is a phloem-affecting disease in citrus that reduces growth and impacts global citrus production. HLB is caused by a phloem-limited bacterium (Candidatus Liberibacter asiaticus). By inhibiting phloem function, HLB stunts sink growth, including the production of new shoots and leaves, and induces hyperaccumulation of foliar starch. HLB induces feedback inhibition of photosynthesis by reducing foliar carbohydrate export. Here, we assessed the relationship of bacterial distribution within the foliage, foliar starch accumulation, and net CO₂ assimilation (A_net ). Because HLB impacts canopy morphology, we developed a chamber to measure whole-shoot A_net to test the effects of HLB at both the leaf and shoot level. Whole-shoot level A_net saturated at high irradiance, and green stems had high photosynthetic rates compared to leaves. Starch accumulation was correlated with bacterial population, and starch was negatively correlated with A_net at the leaf but not at the shoot level. Starch increased initially after infection, then decreased progressively with increasing length of infection. HLB infection reduced A_net at the leaf level but increased it at the whole-shoot level, in association with reduced leaf size and greater relative contribution of stems to the photosynthetic surface area. Although HLB-increased photosynthetic efficiency, total carbon fixed per shoot decreased because photosynthetic surface area was reduced. We conclude that the localized effects of infection on photosynthesis are mitigated by whole-shoot morphological acclimation over time. Stems contribute important proportions of whole-shoot A_net , and these contributions are likely increased by the morphological acclimation induced by HLB.

Plant and soil elemental C:N:P ratios are linked to soil microbial diversity during grassland restoration on the Loess Plateau, China

Plant and soil elemental ratios of carbon (C), nitrogen (N) and phosphorus (P) play a central role in shaping the composition and structure of microbial communities. However, the relationships between plant and soil elemental C:N:P ratios and microbial diversity are still poorly understood. Here, we evaluated the effects of C:N:P ratios in plant-soil systems on microbial diversity in a chronosequence of restored grasslands (1, 5, 10, 15, 25, and 30 years since restoration) on the Loess Plateau. We found that C and N concentrations, C:N and C:P ratios in leaf, root, soil and microbial biomass, bacterial and fungal diversity (Shannon-Wiener index) gradually increased with year since grassland restoration. Microbial C:N:P ratios ranged from 17.8:4.5:1 to 24.3:6.6:1, and C:P ratio increased from 17.8:1 at the 1-year site to 24.3:1 at the 30-year site, indicating the increasing P limitation for soil microorganisms during grassland development. Soil microbial diversity increased with root, soil, and microbial C and N concentrations, and decreased with P concentration (p < 0.05). Structural equation modeling indicated that soil and microbial C:N and N:P ratios had the greatest influences on soil bacterial and fungal diversity, and elemental C:N:P ratios had a greater effect on soil fungal than bacterial diversity. Our findings emphasize the importance of elemental C:N:P ratios on soil microbial diversity, which is critical for formulating policies for sustainable biodiversity conservation in terrestrial ecosystems.

Chlorophyll fluorescence - A tool to assess photosynthetic performance and stress photophysiology in symbiotic marine invertebrates and seaplants

Chlorophyll a fluorescence is increasingly being used as a rapid, non-invasive, sensitive and convenient indicator of photosynthetic performance in marine autotrophs. This review presents the methodology, applications and limitations of chlorophyll fluorescence in marine studies. The various chlorophyll fluorescence tools such as Pulse-Amplitude-Modulated (PAM) and Fast Repetition Rate (FRR) fluorometry used in marine scientific studies are discussed. Various commonly employed chlorophyll fluorescence parameters are elaborated. The application of chlorophyll fluorescence in measuring natural variations, stress, stress tolerance and acclimation/adaptation to changing environment in primary producers such as microalgae, macroalgae, seagrasses and mangroves, and marine symbiotic invertebrates, namely symbiotic sponges, hard corals and sea anemones, kleptoplastic sea slugs and giant clams is critically assessed. Stressors include environmental, biological, physical and chemical ones. The strengths, limitations and future perspectives of the use of chlorophyll fluorescence technique as an assessment tool in symbiotic marine organisms and seaplants are discussed.

Estimating canopy gross primary production by combining phloem stable isotopes with canopy and mesophyll conductances

Gross primary production (GPP) is a key component of the forest carbon cycle. However, our knowledge of GPP at the stand scale remains uncertain, because estimates derived from eddy covariance (EC) rely on semi-empirical modelling and the assumptions of the EC technique are sometimes not fully met. We propose using the sap flux/isotope method as an alternative way to estimate canopy GPP, termed GPP_iso/SF , at the stand scale and at daily resolution. It is based on canopy conductance inferred from sap flux and intrinsic water-use efficiency estimated from the stable carbon isotope composition of phloem contents. The GPP_iso/SF estimate was further corrected for seasonal variations in photosynthetic capacity and mesophyll conductance. We compared our estimate of GPP_iso/SF to the GPP derived from PRELES, a model parameterized with EC data. The comparisons were performed in a highly instrumented, boreal Scots pine forest in northern Sweden, including a nitrogen fertilized and a reference plot. The resulting annual and daily GPP_iso/SF estimates agreed well with PRELES, in the fertilized plot and the reference plot. We discuss the GPP_iso/SF method as an alternative which can be widely applied without terrain restrictions, where the assumptions of EC are not met.

Solar-induced chlorophyll fluorescence and short-term photosynthetic response to drought

Drought is among the most damaging climate extremes, potentially causing significant decline in ecosystem functioning and services at the regional to global scale, thus monitoring of drought events is critically important. Solar-induced chlorophyll fluorescence (SIF) has been found to strongly correlate with gross primary production on the global scale. Recent advances in the remote sensing of SIF allow for large-scale, real-time estimation of photosynthesis using this relationship. However, several studies have used SIF to quantify the impact of drought with mixed results, and the leaf-level mechanisms linking SIF and photosynthesis are unclear, particularly how the relationship may change under drought. We conducted a drought experiment with 2-yr old Populus deltoides. We measured leaf-level gas exchange, SIF, and pulse amplitude modulated (PAM) fluorescence before and during the 1-month drought. We found clear responses of net photosynthesis and stomatal conductance to water stress, however, SIF showed a smaller response to drought. Net photosynthesis (A_net ) and conductance dropped 94% and 95% on average over the drought, while SIF values only decreased slightly (21%). Electron transport rate dropped 64% when compared to the control over the last week of drought, but the electron transport chain did not completely shut down as A_net approached zero. Additionally, SIF yield (SIF_y ) was positively correlated with steady-state fluorescence (F_s ) and negatively correlated with non-photochemical quenching (NPQ; R²  = 0.77). Both F_s and SIF_y , after normalization by the minimum fluorescence from a dark-adapted sample (F_o ), showed a more pronounced drought response, although the results suggest the response is complicated by several factors. Leaf-level experiments can elucidate mechanisms behind large-scale remote sensing observations of ecosystem functioning. The value of SIF as an accurate estimator of photosynthesis may decrease during mild stress events of short duration, especially when the response is primarily stomatal and not fully coupled with the light reactions of photosynthesis. We discuss potential factors affecting the weak SIF response to drought, including upregulation of NPQ, change in internal leaf structure and chlorophyll concentration, and photorespiration. The results suggest that SIF is mainly controlled by the light reactions of photosynthesis, which operate on different timescales than the stomatal response.

Geographical variations in gross primary production and evapotranspiration of paddy rice in the Korean Peninsula

The quantification of canopy photosynthesis and evapotranspiration of crops (ET_c) is essential to appreciate the effects of environmental changes on CO₂ flux and water availability in agricultural ecosystems and crop productivity. This study simulated the canopy photosynthesis and ET processes of paddy rice (Oryza sativa) based on the development of physiological modules (i.e., gross primary production [GPP] and ET_c) and their incorporation into the GRAMI-rice model that uses remote sensing data. We also projected spatiotemporal variations in the GPP, ET, yield, and biomass of paddy rice at maturity using the updated GRAMI-rice model combined with geostationary satellite images to identify the relationships of canopy photosynthesis and ET_c with crop productivity. GPP and ET data for paddy rice were obtained from three KoFlux sites in South Korea in 2015 and 2016. Vegetation indices were acquired from the Geostationary Ocean Color Imager (GOCI) of the Communication Ocean and Meteorological Satellite (COMS) from 2012 to 2017 and integrated into GRAMI-rice. GPP and ET_c estimates using GRAMI-rice were in close agreement with flux tower estimates with Nash-Sutcliffe efficiency ranges of 0.40-0.79 for GPP and 0.49-0.62 for ET_c. Also, GRAMI-rice was reasonably well incorporated with the COMS GOCI imagery and reproduced spatiotemporal variations in the GPP and ET of rice in the Korean peninsula. The current study results demonstrate that the updated GRAMI-rice model with the canopy photosynthesis and ET_c modules is capable of reproducing spatiotemporal variations in CO₂ assimilation and ET of paddy rice at various geographical scales and for regions of interest that are observable by satellite sensors (e.g., inaccessible North Korea).

Identification and evolution of C4 photosynthetic pathway genes in plants

BACKGROUND

NADP-malic enzyme (NAPD-ME), and pyruvate orthophosphate dikinase (PPDK) are important enzymes that participate in C₄ photosynthesis. However, the evolutionary history and forces driving evolution of these genes in C₄ plants are not completely understood.

RESULTS

We identified 162 NADP-ME and 35 PPDK genes in 25 species and constructed respective phylogenetic trees. We classified NADP-ME genes into four branches, A1, A2, B1 and B2, whereas PPDK was classified into two branches in which monocots were in branch I and dicots were in branch II. Analyses of selective pressure on the NAPD-ME and PPDK gene families identified four positively selected sites, including 94H and 196H in the a5 branch of NADP-ME, and 95A and 559E in the e branch of PPDK at posterior probability thresholds of 95%. The positively selected sites were located in the helix and sheet regions. Quantitative RT-PCR (qRT-PCR) analyses revealed that expression levels of 6 NADP-ME and 2 PPDK genes from foxtail millet were up-regulated after exposure to light.

CONCLUSION

This study revealed that positively selected sites of NADP-ME and PPDK evolution in C₄ plants. It provides information on the classification and positive selection of plant NADP-ME and PPDK genes, and the results should be useful in further research on the evolutionary history of C₄ plants.

Photosynthetic Mechanisms of Metaxenia Responsible for Enlargement of Carya cathayensis Fruits at Late Growth Stages

Fruits of hickory (Carya cathayensis) are larger and their peel is greener after interspecific pollination by pecan (Carya illinoinensis; later pp fruits) than after intraspecific pollination by hickory (later ph fruits). Previous studies have found little genetic differences between offspring and their maternal parent, indicating that the observed trait differences between pp and ph fruits are due to metaxenia. Fruit development depends on the amount of photosynthetic assimilate available. Since there is no difference in photosynthesis of the associated leaves between pp and ph fruits, the larger size of the pp fruits might be attributed to changes in fruit photosynthesis caused by the different pollen sources. To elucidate to the photosynthetic mechanisms behind the metaxenia effect on fruit development in hickory, the effects of intraspecific and interspecific pollination regimes were examined in the present study. We observed the photosynthetic capacity in the peel of fruits and the related ecophysiological and morphological traits of both ph and pp fruits over a period of 120 days after pollination. Significant differences in the appearance and dry weight between ph and pp fruits were observed at 50 days after pollination (DAP). More than 70% of dry matter accumulation of the fruits was completed during 60-120 DAP, while the true photosynthetic rate of the associated leaves significantly decreased by about 50% during the same period. In several cell layers of the peel, the number of chloroplasts per cell was significantly higher in pp than in ph fruits. Similarly, the ribulose 1, 5-bisphosphate carboxylase (Rubisco) activity, the total chlorophyll content, and the nitrogen content were all significantly higher in pp than in ph fruits during all growth stages; and all of these physiological quantities were positively correlated with the gross photosynthetic rate of the fruits. We conclude that the enhanced photosynthetic capacity of pp fruits contributes to their fast dry matter accumulation and oil formation. This result will provide a theoretical basis for improving hickory fruit yields in practical cultivation.

An extreme heatwave enhanced the xanthophyll de-epoxidation state in leaves of Eucalyptus trees grown in the field

Heatwaves are becoming more frequent with climate warming and can impact tree growth and reproduction. Eucalyptus parramattensis can cope with an extreme heatwave in the field via transpiratory cooling and enhanced leaf thermal tolerance that protected foliar tissues from photo-inhibition and photo-oxidation during natural midday irradiance. Here, we explored whether changes in foliar carotenoids and/or the xanthophyll cycle state can facilitate leaf acclimation to long-term warming and/or an extreme heatwave event. We found that leaves had similar carotenoid levels when grown for one year under ambient and experimental long-term warming (+ 3 °C) conditions in whole tree chambers. Exposure to a 4-day heatwave (> 43 °C) significantly altered the xanthophyll de-epoxidation state of carotenoids revealing one mechanism by which trees could minimise foliar photo-oxidative damage. The levels of zeaxanthin were significantly higher in both young and old leaves during the heatwave, revealing that violaxanthin de-epoxidation and perhaps de novo zeaxanthin synthesis contributed to enhancement of the xanthophyll cycle state. In a future climate of long-term warming and increased heatwave events, leaves of E. parramattensis will be able to utilise biochemical strategies to alter the xanthophyll cycle state and cope with extreme temperatures under natural solar irradiation.

Effects of water management and cultivar on carbon dynamics, plant productivity and biomass allocation in European rice systems

Water saving techniques, such as alternate wetting and drying (AWD), are becoming a necessity in modern rice farming because of climate change mitigation and growing water use scarcity. Reducing water can vastly reduce methane (CH4) emissions; however, this net climate benefit may be offset by enhanced carbon dioxide (CO2) emissions from soil. The main aims of this study were: to determine the effects of AWD on yield and ecosystem C dynamics, and to establish the underlying mechanistic basis for observed trends in net ecosystem C gain or loss in an Italian rice paddy. We investigated the effects of conventional water management (i.e. conventionally flooded paddy; CF) and AWD on biomass accumulation (aboveground, belowground, grain), key ecosystem C fluxes (net ecosystem exchange (NEE), net primary productivity (NPP), gross primary productivity (GPP), ecosystem respiration (ER), autotrophic respiration (RA), heterotrophic respiration (RH)), and soil organic matter (SOM) decay for four common commercial European rice cultivars. The most significant finding was that neither treatment nor cultivar affected NEE, GPP, ER or SOM decomposition. RA was the dominant contributor to ER for both CF and AWD treatments. Cultivar and treatment affected the total biomass of the rice plants; specifically, with greater root production in CF compared to AWD. Importantly, there was no effect of treatment on the overall yield for any cultivar. Possibly, the wetting-drying cycles may have been insufficient to allow substantial soil C metabolism or there was a lack of labile substrate in the soil. These results imply that AWD systems may not be at risk of enhancing soil C loss, making it a viable solution for climate change mitigation and water conservation. Although more studies are needed, the initial outlook for AWD in Europe is positive; with no net loss of soil C from SOM decomposition, whilst also maintaining yield.

Estimation of a whole plant Q10 to assess seagrass productivity during temperature shifts

Through respiration and photosynthesis, seagrass meadows contribute greatly to carbon and oxygen fluxes in shallow coastal waters. There is increasing concern about how shallow-water primary producers will react to a near-future climate scenario with increased temperature variation. When modelling primary productivity under high temperature variability, Q10 values are commonly used to predict rate changes depending on biophysical factors. Q10 values are often assumed to be constant and around 2.0 (i.e. a doubling of the rate with a temperature increase of 10 °C). We aimed to establish how the gas exchange of seagrass (Zostera marina) tissues at various maturity stages would respond over a broad range of temperatures. Seagrass shoot maturity stage clearly affected respiration and apparent photosynthesis, and the Q10 results indicated a skewed balance between the two processes, with a higher photosynthetic Q10 during periods of elevated temperatures. When estimating whole-plant Q10 in a realistic maximal temperature range, we found that the overall response of a seagrass plant's net O₂ exchange balance can be as much as three to four times higher than under ambient temperatures. Our findings indicate that plant tissue age and temperature should be considered when assessing and modelling carbon and oxygen fluctuations in vegetated coastal areas.

Regulation by FurC in Anabaena Links the Oxidative Stress Response to Photosynthetic Metabolism

The FUR (Ferric Uptake Regulator) family in Anabaena sp. PCC 7120 consists of three paralogs named FurA (Fur), FurB (Zur) and FurC (PerR). furC seems to be an essential gene in the filamentous nitrogen-fixing strain Anabaena sp. PCC 7120, suggesting that it plays a fundamental role in this organism. In order to better understand the functions of FurC in Anabaena, the phenotype of a derivative strain that overexpresses this regulator (EB2770FurC) has been characterized. The furC-overexpressing variant presented alterations in growth rate, morphology and ultrastructure, as well as higher sensitivity to peroxide than Anabaena sp. PCC 7120. Interestingly, the overexpression of furC led to reduced photosynthetic O2 evolution, increased respiratory activity, and had a significant influence in the composition and efficiency of both photosystems. Comparative transcriptional analyses, together with electrophoretic mobility shift assays allowed the identification of different genes directly controlled by FurC, and involved in processes not previously related to PerR proteins, such as the cell division gene ftsZ and the major thylakoid membrane protease ftsH. The rise in the transcription of ftsH in EB2770FurC cells correlated with reduced levels of the D1 protein, which is involved in the PSII repair cycle. Deregulation of the oxidative stress response in EB2770FurC cells led to the identification of novel FurC targets involved in the response to H2O2 through different mechanisms. These results, together with the effect of furC overexpression on the composition, stability and efficiency of the photosynthetic machinery of Anabaena, disclose novel links between PerR proteins, cell division and photosynthesis in filamentous cyanobacteria.

Is NPP proportional to GPP? Waring's hypothesis 20 years on

Gross primary production (GPP) is partitioned to autotrophic respiration (Ra) and net primary production (NPP), the latter being used to build plant tissues and synthesize non-structural and secondary compounds. Waring et al. (1998; Net primary production of forests: a constant fraction of gross primary production? Tree Physiol 18:129-134) suggested that a NPP:GPP ratio of 0.47 ± 0.04 (SD) is universal across biomes, tree species and stand ages. Representing NPP in models as a fixed fraction of GPP, they argued, would be both simpler and more accurate than trying to simulate Ra mechanistically. This paper reviews progress in understanding the NPP:GPP ratio in forests during the 20 years since the Waring et al. paper. Research has confirmed the existence of pervasive acclimation mechanisms that tend to stabilize the NPP:GPP ratio and indicates that Ra should not be modelled independently of GPP. Nonetheless, studies indicate that the value of this ratio is influenced by environmental factors, stand age and management. The average NPP:GPP ratio in over 200 studies, representing different biomes, species and forest stand ages, was found to be 0.46, consistent with the central value that Waring et al. proposed but with a much larger standard deviation (±0.12) and a total range (0.22-0.79) that is too large to be disregarded.

Evaluation of the Water Conservation Function of Different Forest Types in Northeastern China

Water conservation is an important function of forest ecosystems, but it is still unclear which forest types function best in this regard. We investigated the water conservation function indicators including the water-holding rate of branches and leaves (BLwr), water-holding capacity of litter (Lwc), water absorption rate of litter (Lwr), soil infiltration rate (Ir), soil and water content (SWC), soil water storage (SWS), and soil organic matter (SOM) accumulation of five forest types (Larix gmelinii forests, Pinus koraiensis forests, Robinia pseudoacacia forests, Pinus tabulaeformis forests, and mixed forests) and evaluated them using the gray correlation method (GCM). The results indicate that the BLwr of five stands in the study area varied from 18.3% to 33.5%. The SWC and SWS of the R. pseudoacacia stand were 13.76% and 178.9 mm, respectively, which was significantly higher than that of the other stands (p < 0.05). The SOM was similar for the R. pseudoacacia (0.23%), mixed forest (0.22%), and L. gmelinii (0.22%) sites. The BLwr, Lwc, Lwr, SWC, and SWS values of broad-leaved tree species were higher than those of the mixed species, followed by those for coniferous tree species. Soil infiltration rate followed the order L. gmelinii > P. koraiensis > mixed forest > P. tabulaeformis > R. pseudoacacia. Based on our results, the R. pseudoacacia stand had the highest water conservation ability, while the lowest performance was found for the P. tabuliformis site. This suggests that, in order to enhance the water conservation function of forests in northeastern China, the focus should be on the establishment of R. pseudoacacia forests.

Gross Primary Productivity of Four European Ecosystems Constrained by Joint CO2 and COS Flux Measurements

Gross primary productivity (GPP), the gross uptake of carbon dioxide (CO2) by plant photosynthesis, is the primary driver of the land carbon sink, which presently removes around one quarter of the anthropogenic CO2 emissions each year. GPP, however, cannot be measured directly and the resulting uncertainty undermines our ability to project the magnitude of the future land carbon sink. Carbonyl sulfide (COS) has been proposed as an independent proxy for GPP as it diffuses into leaves in a fashion very similar to CO2, but in contrast to the latter is generally not emitted. Here we use concurrent ecosystem-scale flux measurements of CO2 and COS at four European biomes for a joint constraint on CO2 flux partitioning. The resulting GPP estimates generally agree with classical approaches relying exclusively on CO2 fluxes but indicate a systematic underestimation under low light conditions, demonstrating the importance of using multiple approaches for constraining present-day GPP.

Soil carbonyl sulfide exchange in relation to microbial community composition: insights from a managed grassland soil amendment experiment

The viability of carbonyl sulfide (COS) measurements for partitioning ecosystem-scale net carbon dioxide (CO2) fluxes into photosynthesis and respiration critically depends on our knowledge of non-leaf sinks and sources of COS in ecosystems. We combined soil gas exchange measurements of COS and CO2 with next-generation sequencing technology (NGS) to investigate the role of soil microbiota for soil COS exchange. We applied different treatments (litter and glucose addition, enzyme inhibition and gamma sterilization) to soil samples from a temperate grassland to manipulate microbial composition and activity. While untreated soil was characterized by consistent COS uptake, other treatments reduced COS uptake and even turned the soil into a net COS source. Removing biotic processes through sterilization led to positive or zero fluxes. We used NGS to link changes in the COS response to alterations in the microbial community composition, with bacterial data having a higher explanatory power for the measured COS fluxes than fungal data. We found that the genera Arthrobacter and Streptomyces were particularly abundant in samples exhibiting high COS emissions. Our results indicate co-occurring abiotic production and biotic consumption of COS in untreated soil, the latter linked to carbonic anhydrase activity, and a strong dependency of the COS flux on the activity, identity, abundance of and substrate available to microorganisms.

Current and emerging methodologies for estimating carbon sequestration in agricultural soils: A review

This review covers the current and emerging analytical methods used in laboratory, field, landscape and regional contexts for measuring soil organic carbon (SOC) sequestration in agricultural soil. Soil depth plays an important role in estimating SOC sequestration. Selecting appropriate sampling design, depth of soil, use of proper analytical methods and base line selection are prerequisites for estimating accurately the soil carbon stocks. Traditional methods of wet digestion and dry combustion (DC) are extensively used for routine laboratory analysis; the latter is considered to be the "gold standard" and superior to the former for routine laboratory analysis. Recent spectroscopic techniques can measure SOC stocks in laboratory and in-situ even up to a deeper depth. Aerial spectroscopy using multispectral and/or hyperspectral sensors located on aircraft, unmanned aerial vehicles (UAVs) or satellite platforms can measure surface soil organic carbon. Although these techniques' current precision is low, the next generation hyperspectral sensor with improved signal noise ratio will further improve the accuracy of prediction. At the ecosystem level, carbon balance can be estimated directly using the eddy-covariance approach and indirectly by employing agricultural life cycle analysis (LCA). These methods have tremendous potential for estimating SOC. Irrespective of old or new approaches, depending on the resources and research needed, they occupy a unique place in soil carbon and climate research. This paper highlights the overview, potential limitations of various scale-dependent techniques for measuring SOC sequestration in agricultural soil.

Photosynthetic activity of reproductive organs

During seed development, carbon is reallocated from maternal tissues to support germination and subsequent growth. As this pool of resources is depleted post-germination, the plant begins autotrophic growth through leaf photosynthesis. Photoassimilates derived from the leaf are used to sustain the plant and form new organs, including other vegetative leaves, stems, bracts, flowers, fruits, and seeds. In contrast to the view that reproductive tissues act only as resource sinks, many studies demonstrate that flowers, fruits, and seeds are photosynthetically active. The photosynthetic contribution to development is variable between these reproductive organs and between species. In addition, our understanding of the developmental control of photosynthetic activity in reproductive organs is vastly incomplete. A further complication is that reproductive organ photosynthesis (ROP) appears to be particularly important under suboptimal growth conditions. Therefore, the topic of ROP presents the community with a challenge to integrate the fields of photosynthesis, development, and stress responses. Here, we attempt to summarize our understanding of the contribution of ROP to development and the molecular mechanisms underlying its control.

Widespread inhibition of daytime ecosystem respiration

The global land surface absorbs about a third of anthropogenic emissions each year, due to the difference between two key processes: ecosystem photosynthesis and respiration. Despite the importance of these two processes, it is not possible to measure either at the ecosystem scale during the daytime. Eddy-covariance measurements are widely used as the closest 'quasi-direct' ecosystem-scale observation from which to estimate ecosystem photosynthesis and respiration. Recent research, however, suggests that current estimates may be biased by up to 25%, due to a previously unaccounted for process: the inhibition of leaf respiration in the light. Yet the extent of inhibition remains debated, and implications for estimates of ecosystem-scale respiration and photosynthesis remain unquantified. Here, we quantify an apparent inhibition of daytime ecosystem respiration across the global FLUXNET eddy-covariance network and identify a pervasive influence that varies by season and ecosystem type. We develop partitioning methods that can detect an apparent ecosystem-scale inhibition of daytime respiration and find that diurnal patterns of ecosystem respiration might be markedly different than previously thought. The results call for the re-evaluation of global terrestrial carbon cycle models and also suggest that current global estimates of photosynthesis and respiration may be biased, some on the order of magnitude of anthropogenic fossil fuel emissions.

Modelling carbon sources and sinks in terrestrial vegetation

Contents Summary 652 I. Introduction 652 II. Discrepancy in predicting the effects of rising [CO₂ ] on the terrestrial C sink 655 III. Carbon and nutrient storage in plants and its modelling 656 IV. Modelling the source and the sink: a plant perspective 657 V. Plant-scale water and Carbon flux models 660 VI. Challenges for the future 662 Acknowledgements 663 Authors contributions 663 References 663 SUMMARY: The increase in atmospheric CO₂ in the future is one of the most certain projections in environmental sciences. Understanding whether vegetation carbon assimilation, growth, and changes in vegetation carbon stocks are affected by higher atmospheric CO₂ and translating this understanding in mechanistic vegetation models is of utmost importance. This is highlighted by inconsistencies between global-scale studies that attribute terrestrial carbon sinks to CO₂ stimulation of gross and net primary production on the one hand, and forest inventories, tree-scale studies, and plant physiological evidence showing a much less pronounced CO₂ fertilization effect on the other hand. Here, we review how plant carbon sources and sinks are currently described in terrestrial biosphere models. We highlight an uneven representation of complexity between the modelling of photosynthesis and other processes, such as plant respiration, direct carbon sinks, and carbon allocation, largely driven by available observations. Despite a general lack of data on carbon sink dynamics to drive model improvements, ways forward toward a mechanistic representation of plant carbon sinks are discussed, leveraging on results obtained from plant-scale models and on observations geared toward model developments.

Environmental controls on light inhibition of respiration and leaf and canopy daytime carbon exchange in a temperate deciduous forest

Uncertainty in the estimation of daytime ecosystem carbon cycling due to the light inhibition of leaf respiration and photorespiration, and how these small fluxes vary through the growing season in the field, remains a confounding element in calculations of gross primary productivity and ecosystem respiration. Our study focuses on how phenology, short-term temperature changes and canopy position influence leaf-level carbon exchange in Quercus rubra L. (red oak) at Harvard Forest in central Massachusetts, USA. Using leaf measurements and eddy covariance, we also quantify the effect of light inhibition on estimates of daytime respiration at leaf and ecosystem scales. Measured rates of leaf respiration in the light and dark were highest in the early growing season and declined in response to 10-day prior air temperatures (P < 0.01), evidence of within-season thermal acclimation. Leaf respiration was significantly inhibited by light (27.1 ± 2.82% inhibited across all measurements), and this inhibition varied with the month of measurement; greater inhibition was observed in mid-summer leaves compared with early- and late-season leaves. Increases in measurement temperature led to higher rates of respiration and photorespiration, though with a less pronounced positive effect on photosynthesis; as a result, carbon-use efficiency declined with increasing leaf temperature. Over the growing season when we account for seasonally variable light inhibition and basal respiration rates, our modeling approaches found a cumulative 12.9% reduction of leaf-level respiration and a 12.8% reduction of canopy leaf respiration, resulting in a 3.7% decrease in total ecosystem respiration compared with estimates that do not account for light inhibition in leaves. Our study sheds light on the environmental controls of the light inhibition of daytime leaf respiration and how integrating this phenomenon and other small fluxes can reduce uncertainty in current and future projections of terrestrial carbon cycling.

Effects of ultraviolet radiation and nutrient level on the physiological response and organic matter release of the scleractinian coral Pocillopora damicornis following thermal stress

Understanding which factors enhance or mitigate the impact of high temperatures on corals is crucial to predict the severity of coral bleaching worldwide. On the one hand, global warming is usually associated with high ultraviolet radiation levels (UVR), and surface water nutrient depletion due to stratification. On the other hand, eutrophication of coastal reefs increases levels of inorganic nutrients and decreases UVR, so that the effect of different combinations of these stressors on corals is unknown. In this study, we assessed the individual and crossed effects of high temperature, UVR and nutrient level on the key performance variables of the reef building coral Pocillopora damicornis. We found that seawater warming was the major stressor, which induced bleaching and impaired coral photosynthesis and calcification in all nutrient and UVR conditions. The strength of this effect however, was nutrient dependent. Corals maintained in nutrient-depleted conditions experienced the highest decrease in net photosynthesis under thermal stress, while nutrient enrichment (3 μM NO3- and 1 μM PO4+) slightly limited the negative impact of temperature through enhanced protein content, photosynthesis and respiration rates. UVR exposure had only an effect on total nitrogen release rates, which significantly decreased under normal growth conditions and tended to decrease also under thermal stress. This result suggests that increased level of UVR will lead to significant changes in the nutrient biogeochemistry of surface reef waters. Overall, our results show that environmental factors have different and interactive effects on each of the coral's physiological parameters, requiring multifactorial approaches to predict the future of coral reefs.

Bigleaf-An R package for the calculation of physical and physiological ecosystem properties from eddy covariance data

We present the R package bigleaf (version 0.6.5), an open source toolset for the derivation of meteorological, aerodynamic, and physiological ecosystem properties from eddy covariance (EC) flux observations and concurrent meteorological measurements. A 'big-leaf' framework, in which vegetation is represented as a single, uniform layer, is employed to infer bulk ecosystem characteristics top-down from the measured fluxes. Central to the package is the calculation of a bulk surface/canopy conductance (Gs/Gc) and a bulk aerodynamic conductance (Ga), with the latter including formulations for the turbulent and canopy boundary layer components. The derivation of physical land surface characteristics such as surface roughness parameters, wind profile, aerodynamic and radiometric surface temperature, surface vapor pressure deficit (VPD), potential evapotranspiration (ET), imposed and equilibrium ET, as well as vegetation-atmosphere decoupling coefficients, is described. The package further provides calculation routines for physiological ecosytem properties (stomatal slope parameters, stomatal sensitivity to VPD, bulk intercellular CO2 concentration, canopy photosynthetic capacity), energy balance characteristics (closure, biochemical energy), ancillary meteorological variables (psychrometric constant, saturation vapor pressure, air density, etc.), customary unit interconversions and data filtering. The target variables can be calculated with a different degree of complexity, depending on the amount of available site-specific information. The utilities of the package are demonstrated for three single-level (above-canopy) eddy covariance sites representing a temperate grassland, a temperate needle-leaf forest, and a Mediterranean evergreen broadleaf forest. The routines are further tested for a two-level EC site (tree and grass layer) located in a Mediterranean oak savanna. The limitations and the ecophysiological interpretation of the derived ecosystem properties are discussed and practical guidelines are given. The package provides the basis for a consistent, physically sound, and reproducible characterization of biometeorological conditions and ecosystem physiology, and is applicable to EC sites across vegetation types and climatic conditions with minimal ancillary data requirements.

Measuring the dynamic photosynthome

Background

Photosynthesis underpins plant productivity and yet is notoriously sensitive to small changes in environmental conditions, meaning that quantitation in nature across different time scales is not straightforward. The 'dynamic' changes in photosynthesis (i.e. the kinetics of the various reactions of photosynthesis in response to environmental shifts) are now known to be important in driving crop yield.

Scope

It is known that photosynthesis does not respond in a timely manner, and even a small temporal 'mismatch' between a change in the environment and the appropriate response of photosynthesis toward optimality can result in a fall in productivity. Yet the most commonly measured parameters are still made at steady state or a temporary steady state (including those for crop breeding purposes), meaning that new photosynthetic traits remain undiscovered.

Conclusions

There is a great need to understand photosynthesis dynamics from a mechanistic and biological viewpoint especially when applied to the field of 'phenomics' which typically uses large genetically diverse populations of plants. Despite huge advances in measurement technology in recent years, it is still unclear whether we possess the capability of capturing and describing the physiologically relevant dynamic features of field photosynthesis in sufficient detail. Such traits are highly complex, hence we dub this the 'photosynthome'. This review sets out the state of play and describes some approaches that could be made to address this challenge with reference to the relevant biological processes involved.

Improving models of photosynthetic thermal acclimation: Which parameters are most important and how many should be modified?

Photosynthetic temperature acclimation could strongly affect coupled vegetation-atmosphere feedbacks in the global carbon cycle, especially as the climate warms. Thermal acclimation of photosynthesis can be modelled as changes in the parameters describing the direct effect of temperature on photosynthetic capacity (i.e., activation energy, E_a ; deactivation energy, H_d ; entropy parameter, ΔS) or the basal value of photosynthetic capacity (i.e., photosynthetic capacity measured at 25°C). However, the impact of acclimating these parameters (individually or in combination) on vegetative carbon gain is relatively unexplored. Here we compare the ability of 66 photosynthetic temperature acclimation scenarios to improve the ability of a spatially explicit canopy carbon flux model, MAESTRA, to predict eddy covariance data from a loblolly pine forest. We show that: (1) incorporating seasonal temperature acclimation of basal photosynthetic capacity improves the model's ability to capture seasonal changes in carbon fluxes and outperforms acclimation of other single factors (i.e., E_a or ΔS alone); (2) multifactor scenarios of photosynthetic temperature acclimation provide minimal (if any) improvement in model performance over single factor acclimation scenarios; (3) acclimation of E_a should be restricted to the temperature ranges of the data from which the equations are derived; and (4) model performance is strongly affected by the H_d parameter. We suggest that a renewed effort be made into understanding whether basal photosynthetic capacity, E_a , H_d and ΔS co-acclimate across broad temperature ranges to determine whether and how multifactor thermal acclimation of photosynthesis occurs.

Decrease in the Photosynthetic Performance of Temperate Grassland Species Does Not Lead to a Decline in the Gross Primary Production of the Ecosystem

Plants, under stressful conditions, can proceed to photosynthetic adjustments in order to acclimatize and alleviate the detrimental impacts on the photosynthetic apparatus. However, it is currently unclear how adjustment of photosynthetic processes under environmental constraints by plants influences CO2 gas exchange at the ecosystem-scale. Over a 2-year period, photosynthetic performance of a temperate grassland ecosystem was characterized by conducting frequent chlorophyll fluorescence (ChlF) measurements on three primary grassland species (Lolium perenne L., Taraxacum sp., and Trifolium repens L.). Ecosystem photosynthetic performance was estimated from measurements performed on the three dominant grassland species weighed based on their relative abundance. In addition, monitoring CO2 fluxes was performed by eddy covariance. The highest decrease in photosynthetic performance was detected in summer, when environmental constraints were combined. Dicot species (Taraxacum sp. and T. repens) presented the strongest capacity to up-regulate PSI and exhibited the highest electron transport efficiency under stressful environmental conditions compared with L. perenne. The decline in ecosystem photosynthetic performance did not lead to a reduction in gross primary productivity, likely because increased light energy was available under these conditions. The carbon amounts fixed at light saturation were not influenced by alterations in photosynthetic processes, suggesting photosynthesis was not impaired. Decreased photosynthetic performance was associated with high respiration flux, but both were influenced by temperature. Our study revealed variation in photosynthetic performance of a grassland ecosystem responded to environmental constraints, but alterations in photosynthetic processes appeared to exhibit a negligible influence on ecosystem CO2 fluxes.

Towards physiologically meaningful water-use efficiency estimates from eddy covariance data

Intrinsic water-use efficiency (iWUE) characterizes the physiological control on the simultaneous exchange of water and carbon dioxide in terrestrial ecosystems. Knowledge of iWUE is commonly gained from leaf-level gas exchange measurements, which are inevitably restricted in their spatial and temporal coverage. Flux measurements based on the eddy covariance (EC) technique can overcome these limitations, as they provide continuous and long-term records of carbon and water fluxes at the ecosystem scale. However, vegetation gas exchange parameters derived from EC data are subject to scale-dependent and method-specific uncertainties that compromise their ecophysiological interpretation as well as their comparability among ecosystems and across spatial scales. Here, we use estimates of canopy conductance and gross primary productivity (GPP) derived from EC data to calculate a measure of iWUE (G₁ , "stomatal slope") at the ecosystem level at six sites comprising tropical, Mediterranean, temperate, and boreal forests. We assess the following six mechanisms potentially causing discrepancies between leaf and ecosystem-level estimates of G₁ : (i) non-transpirational water fluxes; (ii) aerodynamic conductance; (iii) meteorological deviations between measurement height and canopy surface; (iv) energy balance non-closure; (v) uncertainties in net ecosystem exchange partitioning; and (vi) physiological within-canopy gradients. Our results demonstrate that an unclosed energy balance caused the largest uncertainties, in particular if it was associated with erroneous latent heat flux estimates. The effect of aerodynamic conductance on G₁ was sufficiently captured with a simple representation. G₁ was found to be less sensitive to meteorological deviations between canopy surface and measurement height and, given that data are appropriately filtered, to non-transpirational water fluxes. Uncertainties in the derived GPP and physiological within-canopy gradients and their implications for parameter estimates at leaf and ecosystem level are discussed. Our results highlight the importance of adequately considering the sources of uncertainty outlined here when EC-derived water-use efficiency is interpreted in an ecophysiological context.

Eddy covariance carbonyl sulphide flux measurements with a quantum cascade laser absorption spectrometer

The trace gas carbonyl sulphide (COS) has lately received growing interest in the eddy covariance (EC) community due to its potential to serve as an independent approach for constraining gross primary production and canopy stomatal conductance. Thanks to recent developments of fast-response high-precision trace gas analysers (e.g. quantum cascade laser absorption spectrometers (QCLAS)), a handful of EC COS flux measurements have been published since 2013. To date, however, a thorough methodological characterisation of QCLAS with regard to the requirements of the EC technique and the necessary processing steps has not been conducted. The objective of this study is to present a detailed characterization of the COS measurement with the Aerodyne QCLAS in the context of the EC technique, and to recommend best EC processing practices for those measurements. Data were collected from May to October 2015 at a temperate mountain grassland in Tyrol, Austria. Analysis of the Allan variance of high-frequency concentration measurements revealed sensor drift to occur under field conditions after an averaging time of around 50 s. We thus explored the use of two high-pass filtering approaches (linear detrending and recursive filtering) as opposed to block averaging and linear interpolation of regular background measurements for covariance computation. Experimental low-pass filtering correction factors were derived from a detailed cospectral analysis. The CO₂ and H₂O flux measurements obtained with the QCLAS were compared against those obtained with a closed-path infrared gas analyser. Overall, our results suggest small, but systematic differences between the various high-pass filtering scenarios with regard to the fraction of data retained in the quality control and flux magnitudes. When COS and CO₂ fluxes are combined in the so-called ecosystem relative uptake rate, systematic differences between the high-pass filtering scenarios largely cancel out, suggesting that this relative metric represents a robust key parameter comparable between studies relying on different post-processing schemes.

Chlorophyll fluorescence tracks seasonal variations of photosynthesis from leaf to canopy in a temperate forest

Accurate estimation of terrestrial gross primary productivity (GPP) remains a challenge despite its importance in the global carbon cycle. Chlorophyll fluorescence (ChlF) has been recently adopted to understand photosynthesis and its response to the environment, particularly with remote sensing data. However, it remains unclear how ChlF and photosynthesis are linked at different spatial scales across the growing season. We examined seasonal relationships between ChlF and photosynthesis at the leaf, canopy, and ecosystem scales and explored how leaf-level ChlF was linked with canopy-scale solar-induced chlorophyll fluorescence (SIF) in a temperate deciduous forest at Harvard Forest, Massachusetts, USA. Our results show that ChlF captured the seasonal variations of photosynthesis with significant linear relationships between ChlF and photosynthesis across the growing season over different spatial scales (R²  = 0.73, 0.77, and 0.86 at leaf, canopy, and satellite scales, respectively; P < 0.0001). We developed a model to estimate GPP from the tower-based measurement of SIF and leaf-level ChlF parameters. The estimation of GPP from this model agreed well with flux tower observations of GPP (R²  = 0.68; P < 0.0001), demonstrating the potential of SIF for modeling GPP. At the leaf scale, we found that leaf F_q '/F_m ', the fraction of absorbed photons that are used for photochemistry for a light-adapted measurement from a pulse amplitude modulation fluorometer, was the best leaf fluorescence parameter to correlate with canopy SIF yield (SIF/APAR, R²  = 0.79; P < 0.0001). We also found that canopy SIF and SIF-derived GPP (GPP_SIF ) were strongly correlated to leaf-level biochemistry and canopy structure, including chlorophyll content (R²  = 0.65 for canopy GPP_SIF and chlorophyll content; P < 0.0001), leaf area index (LAI) (R²  = 0.35 for canopy GPP_SIF and LAI; P < 0.0001), and normalized difference vegetation index (NDVI) (R²  = 0.36 for canopy GPP_SIF and NDVI; P < 0.0001). Our results suggest that ChlF can be a powerful tool to track photosynthetic rates at leaf, canopy, and ecosystem scales.

Revisiting the choice of the driving temperature for eddy covariance CO2 flux partitioning

So-called CO₂ flux partitioning algorithms are widely used to partition the net ecosystem CO₂ exchange into the two component fluxes, gross primary productivity and ecosystem respiration. Common CO₂ flux partitioning algorithms conceptualize ecosystem respiration to originate from a single source, requiring the choice of a corresponding driving temperature. Using a conceptual dual-source respiration model, consisting of an above- and a below-ground respiration source each driven by a corresponding temperature, we demonstrate that the typical phase shift between air and soil temperature gives rise to a hysteresis relationship between ecosystem respiration and temperature. The hysteresis proceeds in a clockwise fashion if soil temperature is used to drive ecosystem respiration, while a counter-clockwise response is observed when ecosystem respiration is related to air temperature. As a consequence, nighttime ecosystem respiration is smaller than daytime ecosystem respiration when referenced to soil temperature, while the reverse is true for air temperature. We confirm these qualitative modelling results using measurements of day and night ecosystem respiration made with opaque chambers in a short-statured mountain grassland. Inferring daytime from nighttime ecosystem respiration or vice versa, as attempted by CO₂ flux partitioning algorithms, using a single-source respiration model is thus an oversimplification resulting in biased estimates of ecosystem respiration. We discuss the likely magnitude of the bias, options for minimizing it and conclude by emphasizing that the systematic uncertainty of gross primary productivity and ecosystem respiration inferred through CO₂ flux partitioning needs to be better quantified and reported.

In situ soil COS exchange of a temperate mountain grassland under simulated drought

During recent years, carbonyl sulfide (COS), a trace gas with a similar diffusion pathway into leaves as carbon dioxide (CO2), but with no known "respiration-like" leaf source, has been discussed as a promising new approach for partitioning net ecosystem-scale CO2 fluxes into photosynthesis and respiration. The utility of COS for flux partitioning at the ecosystem scale critically depends on the understanding of non-leaf sources and sinks of COS. This study assessed the contribution of the soil to ecosystem-scale COS fluxes under simulated drought conditions at temperate grassland in the Central Alps. We used transparent steady-state flow-through chambers connected to a quantum cascade laser spectrometer to measure the COS and CO2 gas exchange between the soil surface and the atmosphere. Soils were a source of COS during the day, emissions being mainly driven by incoming solar radiation and to a lesser degree soil temperature. Soil water content had a negligible influence on soil COS exchange and thus the drought and control treatment were statistically not significantly different. Overall, daytime fluxes were large (12.5 ± 13.8 pmol m-2 s-1) in their magnitude and consistently positive compared to the previous studies, which predominantly used dark chambers. Nighttime measurements revealed soil COS fluxes around zero, as did measurements with darkened soil chambers during daytime reinforcing the importance of incoming solar radiation. Our results suggest that abiotic drivers play a key role in controlling in situ soil COS fluxes of the investigated grassland.

Atmospheric CO2 mole fraction affects stand-scale carbon use efficiency of sunflower by stimulating respiration in light

Plant carbon-use-efficiency (CUE), a key parameter in carbon cycle and plant growth models, quantifies the fraction of fixed carbon that is converted into net primary production rather than respired. CUE has not been directly measured, partly because of the difficulty of measuring respiration in light. Here, we explore if CUE is affected by atmospheric CO₂ . Sunflower stands were grown at low (200 μmol mol^-1 ) or high CO₂ (1000 μmol mol^-1 ) in controlled environment mesocosms. CUE of stands was measured by dynamic stand-scale ¹³ C labelling and partitioning of photosynthesis and respiration. At the same plant age, growth at high CO₂ (compared with low CO₂ ) led to 91% higher rates of apparent photosynthesis, 97% higher respiration in the dark, yet 143% higher respiration in light. Thus, CUE was significantly lower at high (0.65) than at low CO₂ (0.71). Compartmental analysis of isotopic tracer kinetics demonstrated a greater commitment of carbon reserves in stand-scale respiratory metabolism at high CO₂ . Two main processes contributed to the reduction of CUE at high CO₂ : a reduced inhibition of leaf respiration by light and a diminished leaf mass ratio. This work highlights the relevance of measuring respiration in light and assessment of the CUE response to environment conditions.

On the energy balance closure and net radiation in complex terrain

In complex, sloping terrain, horizontal measurements of net radiation are not reflective of the radiative energy available for the conductive and convective heat exchange of the underlying surface. Using data from a grassland site on a mountain slope characterised by spatial heterogeneity in inclination and aspect, we tested the hypothesis that a correction of the horizontal net radiation measurements which accounts for the individual footprint contributions of the various surfaces to the measured sensible and latent heat eddy covariance fluxes will yield more realistic slope-parallel net radiation estimates compared to a correction based on the average inclination and aspect of the footprint. Our main result is that both approaches led to clear, but very similar improvements in the phase between available energy and the sum of the latent and sensible heat fluxes. As a consequence the variance in the sum of latent and sensible heat flux explained by available radiation improved by >10 %, while energy balance closure improved only slightly. This is shown to be mainly due to the average inclination and aspect corresponding largely with the inclination and aspect of the main flux source area in combination with a limited sensitivity of the slope correction to small angular differences in, particularly, inclination and aspect. We conclude with a discussion of limitations of the present approach and future research directions.