Relative functional and optical absorption cross-sections of PSII and other photosynthetic parameters monitored in situ, at a distance with a time resolution of a few seconds, using a prototype light induced fluorescence transient (LIFT) device

The Fitting of the OJ Phase of Chlorophyll Fluorescence Induction Based on an Analytical Solution and Its Application in Urban Heat Island Research

Chlorophyll (Chl) fluorescence induction (FI) upon a dark-light transition has been widely analyzed to derive information on initial events of energy conversion and electron transfer in photosystem II (PSII). However, currently, there is no analytical solution to the differential equation of QA reduction kinetics, raising a doubt about the fitting of FI by numerical iteration solution. We derived an analytical solution to fit the OJ phase of FI, thereby yielding estimates of three parameters: the functional absorption cross-section of PSII (σPSII), a probability parameter that describes the connectivity among PSII complexes (p), and the rate coefficient for QA- oxidation (kox). We found that σPSII, p, and kox exhibited dynamic changes during the transition from O to J. We postulated that in high excitation light, some other energy dissipation pathways may vastly outcompete against excitation energy transfer from a closed PSII trap to an open PSII, thereby giving the impression that connectivity seemingly does not exist. We also conducted a case study on the urban heat island effect on the heat stability of PSII using our method and showed that higher-temperature-acclimated leaves had a greater σPSII, lower kox, and a tendency of lower p towards more shade-type characteristics.

Field phenotyping of ten wheat cultivars under elevated CO2 shows seasonal differences in chlorophyll fluorescence, plant height and vegetation indices

In the context of climate change and global sustainable development goals, future wheat cultivation has to master various challenges at a time, including the rising atmospheric carbon dioxide concentration ([CO2]). To investigate growth and photosynthesis dynamics under the effects of ambient (~434 ppm) and elevated [CO2] (~622 ppm), a Free-Air CO2 Enrichment (FACE) facility was combined with an automated phenotyping platform and an array of sensors. Ten modern winter wheat cultivars (Triticum aestivum L.) were monitored over a vegetation period using a Light-induced Fluorescence Transient (LIFT) sensor, ground-based RGB cameras and a UAV equipped with an RGB and multispectral camera. The LIFT sensor enabled a fast quantification of the photosynthetic performance by measuring the operating efficiency of Photosystem II (Fq'/Fm') and the kinetics of electron transport, i.e. the reoxidation rates Fr1' and Fr2'. Our results suggest that elevated [CO2] significantly increased Fq'/Fm' and plant height during the vegetative growth phase. As the plants transitioned to the senescence phase, a pronounced decline in Fq'/Fm' was observed under elevated [CO2]. This was also reflected in the reoxidation rates Fr1' and Fr2'. A large majority of the cultivars showed a decrease in the harvest index, suggesting a different resource allocation and indicating a potential plateau in yield progression under e[CO2]. Our results indicate that the rise in atmospheric [CO2] has significant effects on the cultivation of winter wheat with strong manifestation during early and late growth.

A quantum trajectory picture of single photon absorption and energy transport in photosystem II

We use quantum trajectory theory to study the dynamics of the first step in photosynthesis for a single photon interacting with photosystem II (PSII). By considering individual trajectories we are able to look beyond the ensemble average dynamics to compute the PSII system evolution conditioned upon individual photon counting measurements. Measurements of the transmitted photon beam strongly affects the system state, since detection of an outgoing photon confirms that the PSII must be in the electronic ground state, while a null measurement implies it is in an excited electronic state. We show that under ideal conditions, observing the null result transforms a state with a low excited state population to a state with nearly all population contained in the excited states. We study the PSII dynamics conditioned on such photon counting for both a pure excitonic model of PSII and a more realistic model with exciton-phonon coupling to a dissipative phononic environment. In the absence of such coupling, we show that the measured fluorescence rates show oscillations constituting a photon-counting witness of excitonic coherence. Excitonic coupling to the phonon environment has a strong effect on the observed rates of fluorescence, damping the oscillations. Addition of non-radiative decay and incoherent transitions to radical pair states in the reaction center to the phononic model allows extraction of a quantum efficiency of 92.5% from the long-time evolution, consistent with bulk experimental measurements.

The diversity and ecology of Symbiodiniaceae: A traits-based review

Among the most successful microeukaryotes to form mutualisms with animals are dinoflagellates in the family Symbiodiniaceae. These photosynthetic symbioses drive significant primary production and are responsible for the formation of coral reef ecosystems but are particularly sensitive when environmental conditions become extreme. Annual episodes of widespread coral bleaching (disassociation of the mutualistic partnership) and mortality are forecasted from the year 2060 under current trends of ocean warming. However, host cnidarians and dinoflagellate symbionts display exceptional genetic and functional diversity, and meaningful predictions of the future that embrace this biological complexity are difficult to make. A recent move to trait-based biology (and an understanding of how traits are shaped by the environment) has been adopted to move past this problem. The aim of this review is to: (1) provide an overview of the major cnidarian lineages that are symbiotic with Symbiodiniaceae; (2) summarise the symbiodiniacean genera associated with cnidarians with reference to recent changes in taxonomy and systematics; (3) examine the knowledge gaps in Symbiodiniaceae life history from a trait-based perspective; (4) review Symbiodiniaceae trait variation along three abiotic gradients (light, nutrients, and temperature); and (5) provide recommendations for future research of Symbiodiniaceae traits. We anticipate that a detailed understanding of traits will further reveal basic knowledge of the evolution and functional diversity of these mutualisms, as well as enhance future efforts to model stability and change in ecosystems dependent on cnidarian-dinoflagellate organisms.

Advances in field-based high-throughput photosynthetic phenotyping

Gas exchange techniques revolutionized plant research and advanced understanding, including associated fluxes and efficiencies, of photosynthesis, photorespiration, and respiration of plants from cellular to ecosystem scales. These techniques remain the gold standard for inferring photosynthetic rates and underlying physiology/biochemistry, although their utility for high-throughput phenotyping (HTP) of photosynthesis is limited both by the number of gas exchange systems available and the number of personnel available to operate the equipment. Remote sensing techniques have long been used to assess ecosystem productivity at coarse spatial and temporal resolutions, and advances in sensor technology coupled with advanced statistical techniques are expanding remote sensing tools to finer spatial scales and increasing the number and complexity of phenotypes that can be extracted. In this review, we outline the photosynthetic phenotypes of interest to the plant science community and describe the advances in high-throughput techniques to characterize photosynthesis at spatial scales useful to infer treatment or genotypic variation in field-based experiments or breeding trials. We will accomplish this objective by presenting six lessons learned thus far through the development and application of proximal/remote sensing-based measurements and the accompanying statistical analyses. We will conclude by outlining what we perceive as the current limitations, bottlenecks, and opportunities facing HTP of photosynthesis.

Appropriate time interval of PPFD measurement to estimate daily photosynthetic gain

Photosynthetic models sometimes incorporate meteorological elements typically recorded at a time interval of 10 min or 1 h. Because these data are calculated by averaging instantaneous values over time, short-term environmental fluctuations are concealed, which may affect outputs of the model. To assess an appropriate time interval of photosynthetic photon flux density (PPFD) measurement for accurate estimation of photosynthetic gain under open field conditions, we simulated the daily integral net photosynthetic gain using photosynthetic models with or without considering induction kinetics in response to changes in PPFD. Compared with the daily gain calculated from 60-min-interval PPFD data using a steady-state model that ignored the induction kinetics (i.e. a baseline gain), the gains simulated using higher-resolution PPFD data (10-s, 1-min, and 10-min intervals) and using a dynamic model that considered slow induction kinetics were both smaller by ~2%. The gain estimated by the slow dynamic model with 10-s-interval PPFD data was smaller than the baseline gain by more than 5% with a probability of 66%. Thus, the use of low-resolution PPFD data causes overestimation of daily photosynthetic gain in open fields. An appropriate time interval for PPFD measurement is 1 min or shorter to ensure accuracy of the estimates.

Advanced technologies in studying plant photosynthesis: principles and applications

sion="1.0" encoding="utf-8"?> FP Functional Plant Biology Funct. Plant Biol. 1445-4408 1445-4416 CSIRO Publishing 36 Gardiner Road Clayton VIC 3168 Australia FP22050 10.1071/FP22050 Foreword Advanced technologies in studying plant photosynthesis: principles and applications A. Zavafer et al . https://orcid.org/0000-0002-8905-1618 Zavafer Alonso A Fan Dayong B * https://orcid.org/0000-0001-8150-9535 Murakami Keach C Handling Editor Shabala Sergey Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 2001, Australia. Hokkaido Agricultural Research Center (HARC), National Agriculture and Food Research Organization (NARO), 1 Hitsujigaoka, Toyohira, Sapporo 062-8555, Japan. College of Forestry, Beijing Forestry, University, Beijing 100083, China. * Correspondence to: Dayong Fan Hokkaido Agricultural Research Center (HARC), National Agriculture and Food Research Organization (NARO), 1 Hitsujigaoka, Toyohira, Sapporo 062-8555, Japan Email: dayong73fan@163.com 9 May 2022 49 6 Special Issue i iii 9 May 2022 Published: 9 May 2022 © 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing 2022 The Authors The foreword to this special issue on the advanced technologies in studying photosynthesis focuses on the main contributions of Fred Chow, one of the key Australian scientists studying light reactions in plants.

A new method for separate evaluation of PSII with inactive oxygen evolving complex and active D1 by the pulse-amplitude modulated chlorophyll fluorometry

A method that separately quantifies the PSII with inactive oxygen-evolving complex (OEC) and active D1 retaining the primary quinone acceptor (QA )-reducing activity from the PSII with damaged D1 in the leaf was developed using PAM fluorometry. It is necessary to fully reduce QA to obtain F m , the maximum fluorescence. However, QA in PSII with inactive OEC and active D1 would not be fully reduced by a saturating flash. We used the acceptor-side inhibitor DCMU to fully reduce QA . Leaves of cucumber (Cucumis sativus L.) were chilled at 4°C in dark or illuminated with UV-A to selectively inactivate OEC. After these treatments, F v /F m , the maximum quantum yield, in the leaves vacuum-infiltrated with DCMU were greater than those in water-infiltrated leaves. In contrast, when the leaves were illuminated by red light to photodamage D1, F v /F m did not differ between DCMU- and water-infiltrated leaves. These results indicate relevance of the present evaluation of the fraction of PSII with inactive OEC and active D1. Several examinations in the laboratory and glasshouse showed that PSII with inactive OEC and active D1 was only rarely observed. The present simple method would serve as a useful tool to clarify the details of the PSII photoinhibition.

Inhibition of non-photochemical quenching increases functional absorption cross-section of photosystem II as excitation from closed reaction centres is transferred to open centres, facilitating earlier light saturation of photosynthetic electron transport

Induction of non-photochemical quenching (NPQ) of chlorophyll fluorescence in leaves affords photoprotection to the photosynthetic apparatus when, for whatever reason, photon capture in the antennae of photosystems exceeds their capacity to utilise this excitation in photochemistry and ultimately in CO2 assimilation. Here we augment traditional monitoring of NPQ using the fast time resolution, remote and relatively non-intrusive light induced fluorescence transient (LIFT) technique (Kolber et al . 2005 ; Osmond et al . 2017 ) that allows direct measurement of functional (σ'PSII ) and optical cross-sections (a 'PSII ) of PSII in situ , and calculates the half saturation light intensity for ETR (E k ). These parameters are obtained from the saturation and relaxation phases of fluorescence transients elicited by a sequence of 270, high intensity 1 μs flashlets at controlled time intervals over a period of 30 ms in the QA flash at intervals of a few seconds. We report that although σ'PSII undergoes large transient increases after transfer from dark to strong white light (WL) it declines little in steady-state as NPQ is induced in shade- and sun-grown spinach and Arabidopsis genotypes Col , OEpsbs , pgr 5bkg , stn 7 and stn 7/8. In contrast, σ'PSII increases by ~30% when induction of NPQ in spinach is inhibited by dithiothreitol and by inhibition of NPQ in Arabidopsis npq 1, npq 4 and pgr 5. We propose this increase in σ'PSII arises as some excitation from closed PSII reaction centres is transferred to open centres when excitation partitioning to photochemistry (Y II ) and NPQ (Y NP ) declines, and is indicated by an increased excitation dissipation from closed PSII centres (Y NO , including fluorescence emission). Although E k increases following dissipation of excitation as heat when NPQ is engaged, it declines when NPQ is inhibited. Evidently photochemistry becomes more easily light saturated when excitation is transferred from closed RCIIs to open centres with larger σ'PSII . The NPQ mutant pgr 5 is an exception; E k increases markedly in strong light as electron transport QA → PQ and PQ → PSI accelerate and the PQ pool becomes strongly reduced. These novel in situ observations are discussed in the context of contemporary evidence for functional and structural changes in the photosynthetic apparatus during induction of NPQ.

High-throughput field phenotyping reveals genetic variation in photosynthetic traits in durum wheat under drought

Chlorophyll fluorescence (ChlF) is a powerful non-invasive technique for probing photosynthesis. Although proposed as a method for drought tolerance screening, ChlF has not yet been fully adopted in physiological breeding, mainly due to limitations in high-throughput field phenotyping capabilities. The light-induced fluorescence transient (LIFT) sensor has recently been shown to reliably provide active ChlF data for rapid and remote characterisation of plant photosynthetic performance. We used the LIFT sensor to quantify photosynthesis traits across time in a large panel of durum wheat genotypes subjected to a progressive drought in replicated field trials over two growing seasons. The photosynthetic performance was measured at the canopy level by means of the operating efficiency of Photosystem II ( Fq'/Fm' ) and the kinetics of electron transport measured by reoxidation rates ( Fr1' and Fr2' ). Short- and long-term changes in ChlF traits were found in response to soil water availability and due to interactions with weather fluctuations. In mild drought, Fq'/Fm' and Fr2' were little affected, while Fr1' was consistently accelerated in water-limited compared to well-watered plants, increasingly so with rising vapour pressure deficit. This high-throughput approach allowed assessment of the native genetic diversity in ChlF traits while considering the diurnal dynamics of photosynthesis.

Effects of MPK3 and MPK6 kinases on the chloroplast architecture and function induced by cold acclimation in Arabidopsis

Exposure to low, non-freezing temperatures develops freezing tolerance in many plant species. Such process is called cold acclimation. Molecular changes undergone during cold acclimation are orchestrated by signalling networks including MAP kinases. Structure and function of chloroplasts are affected by low temperatures. The aim of this work was to study how the MAP kinases MPK3 and MPK6 are involved in the chloroplast performance upon a long period of cold acclimation. We used Arabidopsis thaliana wild type and mpk3 and mpk6 mutants. Adult plants were acclimated during 7 days at 4 °C and then measurements of PSII performance and chloroplast ultrastructure were carried out. Only the mpk6 acclimated plants showed a high freezing sensitivity. No differences in the PSII function were observed in the plants from the three genotypes exposed to non-acclimated or acclimated conditions. The acclimation of wild-type plants produced severe alterations in the ultrastructure of chloroplast and thylakoids, which was more accentuated in the mpk plants. However, only the mpk6 mutant was unable to internalize the damaged chloroplasts into the vacuole. These results indicate that cold acclimation induces alterations in the chloroplast architecture leading to preserve an optimal performance of PSII. MPK3 and MPK6 are necessary to regulate these morphological changes, but besides, MPK6 is needed to the vacuolization of the damaged chloroplasts, suggesting a role in the chloroplast recycling during cold acclimation. The latter could be quite relevant, since it could explain why this mutant is the only one showing an extremely low freezing tolerance.

Diversity of CAM plant photosynthesis (crassulacean acid metabolism): a tribute to Barry Osmond

This special issue is a tribute to the Australian plant biologist Professor Charles Barry Osmond - Fellow of the Australian Academy of Sciences, the Royal Society of London, and Leopoldina, the German National Academy of Sciences - and his many contributions to our understanding of the biochemistry and physiological ecology of CAM (crassulacean acid metabolism) photosynthesis. This water-conserving photosynthetic pathway is characterised by nocturnal uptake of atmospheric CO2 and typically enables succulent plants to perform and survive in warm semiarid terrestrial and epiphytic habitats. The idea for this issue is to mark the occasion of Barry's 80th birthday in 2019. The foreword highlights some of his outstanding contributions and introduces the research papers of the special issue.

Diurnal dynamics of nonphotochemical quenching in Arabidopsis npq mutants assessed by solar-induced fluorescence and reflectance measurements in the field

Solar-induced fluorescence (SIF) is highly relevant in mapping photosynthesis from remote-sensing platforms. This requires linking SIF to photosynthesis and understanding the role of nonphotochemical quenching (NPQ) mechanisms under field conditions. Hence, active and passive fluorescence were measured in Arabidopsis with altered NPQ in outdoor conditions. Plants with mutations in either violaxanthin de-epoxidase (npq1) or PsbS protein (npq4) exhibited reduced NPQ capacity. Parallel measurements of NPQ, photosystem II efficiency, SIF and spectral reflectance (ρ) were conducted diurnally on one sunny summer day and two consecutive days during a simulated cold spell. Results showed that both npq mutants exhibited higher levels of SIF compared to wild-type plants. Changes in reflectance were related to changes in the violaxanthin-antheraxanthin-zeaxanthin cycle and not to PsbS-mediated conformational changes. When plants were exposed to cold temperatures, rapid onset of photoinhibition strongly quenched SIF in all lines. Using well-characterized Arabidopsis npq mutants, we showed for the first time the quantitative link between SIF, photosynthetic efficiency, NPQ components and leaf reflectance. We discuss the functional potential and limitations of SIF and reflectance measurements for estimating photosynthetic efficiency and NPQ in the field.

Disentangling the photosynthesis performance in japonica rice during natural leaf senescence using OJIP fluorescence transient analysis

Rice undergoes leaf senescence accompanied with grain filling when the plants reach the end of their temporal niche, and a delay in leaf senescence ultimately improves the yield and quality of grain. To estimate the decline in photosynthesis during leaf senescence and to find an efficient and useful tool to identify rice genotypes with a longer duration of active photosynthesis, we examined PSII photosynthetic activity in the flag leaves of japonica rice Shennong265 (SN265) and Beigeng3 (BG3) during leaf senescence using chlorophyll a fluorescence kinetics. The results show that inhibition occurred in the electron transport chains, but the energetic connectivity of PSII units was not affected as dramatically during leaf senescence. PSII reaction centres (RCs) were transformed into 'silent RCs,' and the chlorophyll content decreased during leaf senescence. However the size of the 'economic' antennae increased. Further, the percentage of variation of the specific energy flux parameters can rationally be used to indicate leaf senescence from the perspective of energy balance. Although the performance indices were more sensitive than other functional and structural JIP-test parameters, they still did not serve as an indicator of crop yield.

Global Trends of Usage of Chlorophyll Fluorescence and Projections for the Next Decade

Chlorophyll fluorescence is the most widely used set of techniques to probe photosynthesis and plant stress. Its great versatility has given rise to different routine methods to study plants and algae. The three main technical platforms are pulse amplitude modulation (PAM), fast rise of chlorophyll fluorescence, and fast repetition rate. Solar-induced fluorescence (SIF) has also gained interest in the last few years. Works have compared their advantages and their underlying theory, with many arguments advanced as to which method is the most accurate and useful. To date, no data has assessed the exact magnitude of popularity and influence for each methodology. In this work, we have taken the bibliometrics of the past decade for each of the four platforms, have evaluated the public scientific opinion toward each method, and possibly identified a geographical bias. We used various metrics to assess influence and popularity for the four routine platforms compared in this study and found that, overall, PAM currently has the highest values, although the more recent SIF has increased in popularity rapidly during the last decade. This indicates that PAM is currently one of the fundamental tools in chlorophyll fluorescence.

Photosynthetic sea slugs induce protective changes to the light reactions of the chloroplasts they steal from algae

Sacoglossan sea slugs are able to maintain functional chloroplasts inside their own cells, and mechanisms that allow preservation of the chloroplasts are unknown. We found that the slug Elysia timida induces changes to the photosynthetic light reactions of the chloroplasts it steals from the alga Acetabularia acetabulum. Working with a large continuous laboratory culture of both the slugs (>500 individuals) and their prey algae, we show that the plastoquinone pool of slug chloroplasts remains oxidized, which can suppress reactive oxygen species formation. Slug chloroplasts also rapidly build up a strong proton-motive force upon a dark-to-light transition, which helps them to rapidly switch on photoprotective non-photochemical quenching of excitation energy. Finally, our results suggest that chloroplasts inside E. timida rely on oxygen-dependent electron sinks during rapid changes in light intensity. These photoprotective mechanisms are expected to contribute to the long-term functionality of the chloroplasts inside the slugs.

Plants, algae and a few other organisms rely on a process known as photosynthesis to fuel themselves, as they can harness cellular structures called chloroplasts to convert light into usable energy. Animals typically lack chloroplasts, making them unable to use photosynthesis to power themselves. The sea slug Elysia timida, however, can steal whole chloroplasts from the cells of the algae it consumes: the stolen structures then become part of the cells in the gut of the slug, allowing the animal to gain energy from sunlight.

Once they are in the digestive system of the slug, the chloroplasts survive and keep working for longer than expected. Indeed, these structures are often harmed as a side effect of photosynthesis, but the sea slug does not have the right genes to help repair this damage. In addition, conditions inside animal cells are widely different to the ones found inside algae and plants. It is not clear then how the sea slug extends the lifespan of its chloroplasts by preventing damage caused by sunlight.

To investigate this question, Havurinne and Tyystjärvi compared photosynthesis in sea slugs and the algae they eat. A range of methods, including measuring fluorescence from the chloroplasts, was used: this revealed that the slug changes the inside of the stolen chloroplasts, making them more resistant to damage.

First, when exposed to light the stolen chloroplasts can quickly switch on a mechanism that dissipates light energy to heat, which is less damaging. Second, a molecule that serves as an intermediate during photosynthesis is kept in a ‘safe’ state which prevents it from creating harmful compounds. And finally, additional safeguard molecules ‘deactivate’ compounds that could otherwise mediate damaging reactions. Overall, these measures may reduce the efficiency of the chloroplasts but allow them to keep working for much longer.

Early chloroplasts were probably independent bacteria that were captured and ‘domesticated’ by other cells for their ability to extract energy from the sun. Photosynthesizing sea slugs therefore provide an interesting way to understand some of the challenges of early life. The work by Havurinne and Tyystjärvi may also reveal new ways to harness biological processes such as photosynthesis for energy production in other contexts.

Photosynthesis: basics, history and modelling

BACKGROUND

With limited agricultural land and increasing human population, it is essential to enhance overall photosynthesis and thus productivity. Oxygenic photosynthesis begins with light absorption, followed by excitation energy transfer to the reaction centres, primary photochemistry, electron and proton transport, NADPH and ATP synthesis, and then CO2 fixation (Calvin-Benson cycle, as well as Hatch-Slack cycle). Here we cover some of the discoveries related to this process, such as the existence of two light reactions and two photosystems connected by an electron transport 'chain' (the Z-scheme), chemiosmotic hypothesis for ATP synthesis, water oxidation clock for oxygen evolution, steps for carbon fixation, and finally the diverse mechanisms of regulatory processes, such as 'state transitions' and 'non-photochemical quenching' of the excited state of chlorophyll a.

SCOPE

In this review, we emphasize that mathematical modelling is a highly valuable tool in understanding and making predictions regarding photosynthesis. Different mathematical models have been used to examine current theories on diverse photosynthetic processes; these have been validated through simulation(s) of available experimental data, such as chlorophyll a fluorescence induction, measured with fluorometers using continuous (or modulated) exciting light, and absorbance changes at 820 nm (ΔA820) related to redox changes in P700, the reaction centre of photosystem I.

CONCLUSIONS

We highlight here the important role of modelling in deciphering and untangling complex photosynthesis processes taking place simultaneously, as well as in predicting possible ways to obtain higher biomass and productivity in plants, algae and cyanobacteria.

Time- and reduction-dependent rise of photosystem II fluorescence during microseconds-long inductions in leaves

Lettuce (Lactuca sativa) and benth (Nicotiana benthamiana) leaves were illuminated with 720 nm background light to mix S-states and oxidize electron carriers. Green-filtered xenon flashes of different photon dose were applied and O2 evolution induced by a flash was measured. After light intensity gradient across the leaf was mathematically considered, the flash-induced PSII electron transport (= 4·O2 evolution) exponentially increased with the flash photon dose in any differential layer of the leaf optical density. This proved the absence of excitonic connectivity between PSII units. Time courses of flash light intensity and 680 nm chlorophyll fluorescence emission were recorded. While with connected PSII the sigmoidal fluorescence rise has been explained by quenching of excitation in closed PSII by its open neighbors, in the absence of connectivity the sigmoidicity indicates gradual rise of the fluorescence yield of an individual closed PSII during the induction. Two phases were discerned: the specific fluorescence yield immediately increased from Fo to 1.8Fo in a PSII, whose reaction center became closed; fluorescence yield of the closed PSII was keeping time-dependent rise from 1.8Fo to about 3Fo, approaching the flash fluorescence yield Ff = 0.6Fm during 40 μs. The time-dependent fluorescence rise was resolved from the quenching by 3Car triplets and related to protein conformational change. We suggest that QA reduction induces a conformational change, which by energetic or structural means closes the gate for excitation entrance into the central radical pair trap-efficiently when QB cannot accept the electron, but less efficiently when it can.

Enhanced Algal Photosynthetic Photon Efficiency by Pulsed Light

We present experimental results demonstrating that, relative to continuous illumination, an increase of a factor of 3-10 in the photon efficiency of algal photosynthesis is attainable via the judicious application of pulsed light for light intensities of practical interest (e.g., average-to-peak solar irradiance). We also propose a simple model that can account for all the measurements. The model (1) reflects the essential rate-limiting elements in bioproductivity, (2) incorporates the impact of photon arrival-time statistics, and (3) accounts for how the enhancement in photon efficiency depends on the timescales of light pulsing and photon flux density. The key is avoiding "clogging" of the photosynthetic pathway by properly timing the light-dark cycles experienced by algal cells. We show how this can be realized with pulsed light sources, or by producing pulsed-light effects from continuous illumination via turbulent mixing in dense algal cultures in thin photobioreactors.

Genotype Specific Photosynthesis x Environment Interactions Captured by Automated Fluorescence Canopy Scans Over Two Fluctuating Growing Seasons

Photosynthesis reacts dynamic and in different time scales to changing conditions. Light and temperature acclimation balance photosynthetic processes in a complex interplay with the fluctuating environment. However, due to limitations in the measurements techniques, these acclimations are often described under steady-state conditions leading to inaccurate photosynthesis estimates in the field. Here we analyze the photosynthetic interaction with the fluctuating environment and canopy architecture over two seasons using a fully automated phenotyping system. We acquired over 700,000 chlorophyll fluorescence transients and spectral measurements under semi-field conditions in four crop species including 28 genotypes. As expected, the quantum efficiency of the photosystem II (Fv/Fm in the dark and Fq'/Fm' in the light) was determined by light intensity. It was further significantly affected by spectral indices representing canopy structure effects. In contrast, a newly established parameter, monitoring the efficiency of electron transport (Fr2/Fv in the dark respective Fr2'/Fq' in the light), was highly responsive to temperature (R2 up to 0.75). This parameter decreased with temperature and enabled the detection of cold tolerant species and genotypes. We demonstrated the ability to capture and model the dynamic photosynthesis response to the environment over entire growth seasons. The improved linkage of photosynthetic performance to canopy structure, temperature and cold tolerance offers great potential for plant breeding and crop growth modeling.

Phenotyping Plant Responses to Biotic Stress by Chlorophyll Fluorescence Imaging

Photosynthesis is a pivotal process in plant physiology, and its regulation plays an important role in plant defense against biotic stress. Interactions with pathogens and pests often cause alterations in the metabolism of sugars and sink/source relationships. These changes can be part of the plant defense mechanisms to limit nutrient availability to the pathogens. In other cases, these alterations can be the result of pests manipulating the plant metabolism for their own benefit. The effects of biotic stress on plant physiology are typically heterogeneous, both spatially and temporarily. Chlorophyll fluorescence imaging is a powerful tool to mine the activity of photosynthesis at cellular, leaf, and whole-plant scale, allowing the phenotyping of plants. This review will recapitulate the responses of the photosynthetic machinery to biotic stress factors, from pathogens (viruses, bacteria, and fungi) to pests (herbivory) analyzed by chlorophyll fluorescence imaging both at the lab and field scale. Moreover, chlorophyll fluorescence imagers and alternative techniques to indirectly evaluate photosynthetic traits used at field scale are also revised.

Probing functional and optical cross-sections of PSII in leaves during state transitions using fast repetition rate light induced fluorescence transients

Plants adjust the relative sizes of PSII and PSI antennae in response to the spectral composition of weak light favouring either photosystem by processes known as state transitions (ST), attributed to a discrete antenna migration involving phosphorylation of light-harvesting chlorophyll-protein complexes in PSII. Here for the first time we monitored the extent and dynamics of ST in leaves from estimates of optical absorption cross-section (relative PSII antenna size; aPSII). These estimates were obtained from in situ measurements of functional absorption cross-section (σPSII) and maximum photochemical efficiency of PSII (φPSII); i.e. aPSII = σPSII/φPSII (Kolber et al. 1998) and other parameters from a light induced fluorescence transient (LIFT) device (Osmond et al. 2017). The fast repetition rate (FRR) QA flash protocol of this instrument monitors chlorophyll fluorescence yields with reduced QA irrespective of the redox state of plastoquinone (PQ), as well as during strong ~1 s white light pulses that fully reduce the PQ pool. Fitting this transient with the FRR model monitors kinetics of PSII → PQ, PQ → PSI, and the redox state of the PQ pool in the 'PQ pool control loop' that underpins ST, with a time resolution of a few seconds. All LIFT/FRR criteria confirmed the absence of ST in antenna mutant chlorina-f2 of barley and asLhcb2-12 of Arabidopsis, as well as STN7 kinase mutants stn7 and stn7/8. In contrast, wild-type barley and Arabidopsis genotypes Col, npq1, npq4, OEpsbs, pgr5 bkg and pgr5, showed normal ST. However, the extent of ST (and by implication the size of the phosphorylated LHCII pool participating in ST) deduced from changes in a'PSII and other parameters with reduced QA range up to 35%. Estimates from strong WL pulses in the same assay were only ~10%. The larger estimates of ST from the QA flash are discussed in the context of contemporary dynamic structural models of ST involving formation and participation of PSII and PSI megacomplexes in an 'energetically connected lake' of phosphorylated LHCII trimers (Grieco et al. 2015). Despite the absence of ST, asLhcb2-12 displays normal wild-type modulation of electron transport rate (ETR) and the PQ pool during ST assays, reflecting compensatory changes in antenna LHCIIs in this genotype. Impaired LHCII phosphorylation in stn7 and stn7/8 accelerates ETR from PSII →PQ, over-reducing the PQ pool and abolishing the yield difference between the QA flash and WL pulse, with implications for photochemical and thermal phases of the O-J-I-P transient.

Maximum fluorescence and electron transport kinetics determined by light-induced fluorescence transients (LIFT) for photosynthesis phenotyping

Photosynthetic phenotyping requires quick characterization of dynamic traits when measuring large plant numbers in a fluctuating environment. Here, we evaluated the light-induced fluorescence transient (LIFT) method for its capacity to yield rapidly fluorometric parameters from 0.6 m distance. The close approximation of LIFT to conventional chlorophyll fluorescence (ChlF) parameters is shown under controlled conditions in spinach leaves and isolated thylakoids when electron transport was impaired by anoxic conditions or chemical inhibitors. The ChlF rise from minimum fluorescence (Fo) to maximum fluorescence induced by fast repetition rate (Fm-FRR) flashes was dominated by reduction of the primary electron acceptor in photosystem II (QA). The subsequent reoxidation of QA- was quantified using the relaxation of ChlF in 0.65 ms (Fr1) and 120 ms (Fr2) phases. Reoxidation efficiency of QA- (Fr1/Fv, where Fv = Fm-FRR - Fo) decreased when electron transport was impaired, while quantum efficiency of photosystem II (Fv/Fm) showed often no significant effect. ChlF relaxations of the LIFT were similar to an independent other method. Under increasing light intensities, Fr2'/Fq' (where Fr2' and Fq' represent Fr2 and Fv in the light-adapted state, respectively) was hardly affected, whereas the operating efficiency of photosystem II (Fq'/Fm') decreased due to non-photochemical quenching. Fm-FRR was significantly lower than the ChlF maximum induced by multiple turnover (Fm-MT) flashes. However, the resulting Fv/Fm and Fq'/Fm' from both flashes were highly correlated. The LIFT method complements Fv/Fm with information about efficiency of electron transport. Measurements in situ and from a distance facilitate application in high-throughput and automated phenotyping.

Roadmaps and Detours: Active Chlorophyll- a Assessments of Primary Productivity Across Marine and Freshwater Systems

Assessing phytoplankton productivity over space and time remains a core goal for oceanographers and limnologists. Fast Repetition Rate fluorometry (FRRf) provides a potential means to realize this goal with unprecedented resolution and scale yet has not become the "go-to" method despite high expectations. A major obstacle is difficulty converting electron transfer rates to equivalent rates of C-fixation most relevant for studies of biogeochemical C-fluxes. Such difficulty stems from methodological inconsistencies and our limited understanding of how the electron requirement for C-fixation (Φ_e,C) is influenced by the environment and by differences in the composition and physiology of phytoplankton assemblages. We outline a "roadmap" for limiting methodological bias and to develop a more mechanistic understanding of the ecophysiology underlying Φ_e,C. We 1) re-evaluate core physiological processes governing how microalgae invest photosynthetic electron transport-derived energy and reductant into stored carbon versus alternative sinks. Then, we 2) outline steps to facilitate broader uptake and exploitation of FRRf, which could transform our knowledge of aquatic primary productivity. We argue it is time to 3) revise our historic methodological focus on carbon as the currency of choice, to 4) better appreciate that electron transport fundamentally drives ecosystem biogeochemistry, modulates cell-to-cell interactions, and ultimately modifies community biomass and structure.

Simulation experiments to elucidate variable fluorescence as a potential proxy for bulk microalgal viability from natural water, sediments and biofilms: Implication in ships ballast water management

The variable fluorescence fluorometry measuring microalgal biomass (initial fluorescence - F₀, a chl-a proxy) and photosynthetic efficiency (F_v/F_m) has been suggested as a potential tool in ballast-water assessment. In ballast tank, microalgae can be found in contiguous compartments i.e., in water, sediment, and biofilms. Therefore the utility of F₀ and F_v/F_m depends upon proper background corrections, which is straightforward for water samples but not for sediment and biofilms. This study proposes procedures for correcting F₀ values from sediment and biofilms. Irrespective of the saturation flash protocol used on any sample types the outcome of the results from viable and non-viable microalgae will remain same. Stress experiments (continuous darkness and biocide treatments) confirm that variable fluorescence (F_v) can be used as a potential proxy for viable cells as the values were negligible for non-viable cells and increased with an increase in abundance. Through this study, the utility of F_v and σ_PSII (functional-absorption-cross-section of photosystem II) along with F₀ and F_v/F_m in providing additional information on cell-viability and algal-size group during assessment is discussed. The findings will have implications not only from the perspective of ballast water but also in testing/assays of specific interest (e.g. toxicity, water treatments, antifouling) and ecological studies involving microalgae.

Remote monitoring of dynamic canopy photosynthesis with high time resolution light-induced fluorescence transients

Understanding the net photosynthesis of plant canopies requires quantifying photosynthesis in challenging environments, principally due to the variable light intensities and qualities generated by sunlight interactions with clouds and surrounding foliage. The dynamics of sunflecks and rates of change in light intensity at the beginning and end of sustained light (SL) events makes photosynthetic measurements difficult, especially when dealing with less accessible parts of plant foliage. High time resolved photosynthetic monitoring from pulse amplitude modulated (PAM) fluorometers has limited applicability due to the invasive nature of frequently applied saturating flashes. An alternative approach used here provides remote (<5 m), high time resolution (10 s), PAM equivalent but minimally invasive measurements of photosynthetic parameters. We assessed the efficacy of the QA flash protocol from the Light-Induced Fluorescence Transient (LIFT) technique for monitoring photosynthesis in mature outer canopy leaves of potted Persea americana Mill. cv. Haas (Avocado) trees in a semi-controlled environment and outdoors. Initially we established that LIFT measurements were leaf angle independent between ±40° from perpendicular and moreover, that estimates of 685 nm reflectance (R685) from leaves of similar chlorophyll content provide a species dependent, but reasonable proxy for incident light intensity. Photosynthetic responses during brief light events (≤10 min), and the initial stages of SL events, showed similar declines in the quantum yield of photosystem II (ΦII) with large transient increases in 'constitutive loss processes' (ΦNO) prior to dissipation of excitation by non-photochemical quenching (ΦNPQ). Our results demonstrate the capacity of LIFT to monitor photosynthesis at a distance during highly dynamic light conditions that potentially may improve models of canopy photosynthesis and estimates of plant productivity. For example, generalized additive modelling performed on the 85 dynamic light events monitored identified negative relationships between light event length and ∆ΦII and ∆electron transport rate using either ∆photosynthetically active radiation or ∆R685 as indicators of leaf irradiance.

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.

Living at the margins - The response of deep-water seagrasses to light and temperature renders them susceptible to acute impacts

Seagrasses inhabit environments where light varies at different timescales, nonetheless are acutely sensitive to reductions in light beyond some conditional bounds. Two tropical deep-water seagrasses, Halophila decipiens and Halophila spinulosa, from the Great Barrier Reef were tested for their response to defined light and temperature regimes to identify their growth requirements and potential thresholds of mortality. Species were exposed to two light intensities, saturating (75 μmol photons m^-2 s^-1) and limiting (25 μmol photons m^-2 s^-1) light and two temperature treatments (26 °C and 30 °C) over a four-week period. Wavelength-specific parameters of PSII photochemistry were evaluated for seagrass leaves, as well as shoot density, gas exchange, and pigment content. Both species were sustained under saturating light levels (3.2 mol photons m^-2 d^-1) while limiting light led to decreased shoot density for H. decipiens and H. spinulosa after two and four weeks, respectively. Wavelength-specific photochemistry was also affected under light-limiting treatments for both species while the functional absorption cross section was highly conserved. Photoacclimation and physiological adjustments by either species was not adequate to compensate for reduced irradiance suggesting these plants reside at the margins of their functional limits. As such, relatively short periods of light attenuating events, like dredging or flood plumes, may be detrimental to deep-water seagrass populations.

Kinetics of photosystem II electron transport: a mathematical analysis based on chlorophyll fluorescence induction

The OJDIP rise in chlorophyll fluorescence during induction at different light intensities was mathematically modeled using 24 master equations describing electron transport through photosystem II (PSII) plus ordinary differential equations for electron budgets in plastoquinone, cytochrome f, plastocyanin, photosystem I, and ferredoxin. A novel feature of the model is consideration of electron in- and outflow budgets resulting in changes in redox states of Tyrosine Z, P680, and Q_A as sole bases for changes in fluorescence yield during the transient. Ad hoc contributions by transmembrane electric fields, protein conformational changes, or other putative quenching species were unnecessary to account for primary features of the phenomenon, except a peculiar slowdown of intra-PSII electron transport during induction at low light intensities. The lower than F _m post-flash fluorescence yield F _f was related to oxidized tyrosine Z. The transient J peak was associated with equal rates of electron arrival to and departure from Q_A and requires that electron transfer from Q_A^- to Q_B be slower than that from Q_A^- to Q_B^-. Strong quenching by oxidized P680 caused the dip D. Reduced plastoquinone, a competitive product inhibitor of PSII, blocked electron transport proportionally with its concentration. Electron transport rate indicated by fluorescence quenching was faster than the rate indicated by O₂ evolution, because oxidized donor side carriers quench fluorescence but do not transport electrons. The thermal phase of the fluorescence rise beyond the J phase was caused by a progressive increase in the fraction of PSII with reduced Q_A and reduced donor side.