Do daily and seasonal trends in leaf solar induced fluorescence reflect changes in photosynthesis, growth or light exposure?

Solar induced chlorophyll fluorescence (SIF) emissions of photosynthetically active plants retrieved from space-borne observations have been used to improve models of global primary productivity. However, the relationship between SIF and photosynthesis in diurnal and seasonal cycles is still not fully understood, especially at large spatial scales, where direct measurements of photosynthesis are unfeasible. Motivated by up-scaling potential, this study examined the diurnal and seasonal relationship between SIF and photosynthetic parameters measured at the level of individual leaves. We monitored SIF in two plant species, avocado (Persea Americana) and orange jasmine (Murraya paniculatta), throughout 18 diurnal cycles during the Southern Hemisphere spring, summer and autumn, and compared them with simultaneous measurements of photosynthetic yields, and leaf and global irradiances. Results showed that at seasonal time scales SIF is principally correlated with changes in leaf irradiance, electron transport rates (ETR) and constitutive heat dissipation (YNO; p \u3c 0.001). Multiple regression models of correlations between photosynthetic parameters and SIF at diurnal time scales identified leaf irradiance as the principle predictor of SIF (p \u3c 0.001). Previous studies have identified correlations between photosynthetic yields, ETR and SIF at larger spatial scales, where heterogeneous canopy architecture and landscape spatial patterns influence the spectral and photosynthetic measurements. Although this study found a significant correlation between leaf-measured YNO and SIF, future dedicated up-scaling experiments are required to elucidate if these observations are also found at larger spatial scales

Phylogeny of Three East Antarctic Mosses

Mosses are the key floral component of Antarctic terrestrial ecosystems and provide a model system for the in vivo study of freeze tolerance and ultraviolet-B radiation damage in plants. Furthermore, in the Windmill Islands region of East Antarctica, these plants form part of a long term biodiversity study, using mosses as a proxy for the effects of climate change on Antarctic terrestrial ecosystems. However, morphological similarities between Antarctic moss species may make biodiversity measurements error prone. Furthermore, the species status and phylogenetic relationships of Windmill Islands mosses have not been examined using molecular techniques

Linking spectral signals with novel photosynthetic parameters from the leaf to the canopy

In recent years, airborne spectroradiometers have become sensitive enough to detect subtle increases and decreases in the depth of oxygen absorption lines caused by fluorescence emission from chlorophylls in plants. This fluorescence emission, termed solar induced fluorescence (SIF), is thought to contain information about photosynthesis, which could be utilised in both precision agriculture and dynamic global vegetation models to potentially help mitigate the threat to food security posed by anthropogenic climate change and a growing human population. This PhD thesis is concerned with understanding the photosynthetic information in SIF at spatial scales ranging from the leaf to the canopy. To do this, a novel technique for remotely measuring photosynthesis, known as Light Induced Fluorescence Transients (LIFT), was coupled with a spectroradiometer, allowing for simultaneous measurements of SIF and photosynthesis. Given the novelty of the LIFT instrument for terrestrial photosynthetic measurements, I first provide a detailed overview of the LIFT instrument calibration and operation, and establish nomenclature for LIFT measurements and data processing. The LIFT instrument was then utilized in three field campaigns supported by laboratory measurements of leaf optical properties and pigments. The aims of these three field campaigns was to: 1) characterise LIFT for use in the field, 2) examine the relationship between photosynthesis and SIF on the leaf-level, and 3) understand the relationship between SIF and photosynthesis at different spatial scales..

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 (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 \u27constitutive loss processes\u27 (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

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 prototype light-induced fluorescence transient (LIFT) instrument provides continuous, minimally intrusive, high time resolution (~2 s) assessment of photosynthetic performance in terrestrial plants from up to 2 m. It induces a chlorophyll fluorescence transient by a series of short flashes in a saturation sequence (180 ~1μs flashlets inμs) to achieve near-full reduction of the primary acceptor QA, followed by a relaxation sequence (RQA; 90 flashlets at exponentially increasing intervals over ~30 ms) to observe kinetics of QA re-oxidation. When fitted by the fast repetition rate (FRR) model (Kolber et al. 1998) the QA flash of LIFT/FRR gives smaller values for FmQA from dark adapted leaves than FmPAM from pulse amplitude modulated (PAM) assays. The ratio FmQA/FmPAM resembles the ratio of fluorescence yield at the J/P phases of the classical O-J-I-P transient and we conclude that the difference simply is due to the levels of PQ pool reduction induced by the two techniques. In a strong PAM-analogous WL pulse in the dark monitored by the QA flash of LIFT/FRR φPSIIWL ≈ φPSIIPAM. The QA flash also tracks PQ pool reduction as well as the associated responses of ETR QA → PQ and PQ → PSI, the relative functional (σPSII) and optical absorption (aPSII) cross-sections of PSII in situ with a time resolution of ~2 s as they relax after the pulse. It is impractical to deliver strong WL pulses at a distance in the field but a longer PQ flash from LIFT/FRR also achieves full reduction of PQ pool and delivers φPSIIPQ ≈ φPSIIPAM to obtain PAM-equivalent estimates of ETR and NPQ at a distance. In situ values of σPSII and aPSII from the QA flash with smaller antenna barley (chlorina-f2) and Arabidopsis mutants (asLhcb2-12, ch1-3 Lhcb5) are proportionally similar to those previously reported from in vitro assays. These direct measurements are further validated by changes in antenna size in response to growth irradiance. We illustrate how the QA flash facilitates our understanding of photosynthetic regulation during sun flecks in natural environments at a distance, with a time resolution of a few seconds

Extending Fluspect to simulate xanthophyll driven leaf reflectance dynamics

The xanthophyll cycle regulates the energy flow to photosynthetic reaction centres of plant leaves. Changes in the de-epoxidation state (DEPS) of xanthophyll cycle pigments can be observed as changes in the leaf absorption of light with wavelengths between 500 to 570 nm. These spectral changes can be a good remote sensing indicator of the photosynthetic efficiency, and are traditionally quantified with a two-band physiologically based optical index, the Photochemical Reflectance Index (PRI). In this paper, we present an extension of the plant leaf radiative transfer model Fluspect (Fluspect-CX) that reproduces the spectral changes in a wide band of green reflectance: a radiative transfer analogy to the PRI. The idea of Fluspect-CX is to use in vivo specific absorption coefficients for two extreme states of carotenoids, representing the two extremes of the xanthophyll de-epoxidation, and to describe the intermediate states as a linear mixture of these two states. The \u27photochemical reflectance parameter\u27 (Cx) quantifies the relative proportion of the two states. Fluspect-CX simulates leaf chlorophyll fluorescence (ChlF) excitation-emission matrices, as well as reflectance (R) and transmittance (T) spectra as a function of leaf structure, pigment contents and Cx. We describe the calibration of the model and test its performance using various experimental datasets. Furthermore, we retrieved Cx from optical measurements of various datasets. The retrieved Cx correlates well with xanthophyll DEPS (R2=0.57), as well with non-photochemical quenching (NPQ) of fluorescence (R2=0.78). The correlation with NPQ enabled us to incorporate Fluspect-CX in the model SCOPE to scale the processes to the canopy level. Introducing the dynamic green reflectance into a radiative transfer model provides new means to study chlorophyll fluorescence and PRI dynamics on leaf and canopy scales, which is crucial for the remote sensing

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 (<5m), high time resolution (10 s), PAM equivalent but minimally invasive measurements of photosynthetic parameters. We assessed the efficacy of the Q(A) 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 degrees from perpendicular and moreover, that estimates of 685 nm reflectance (R-685) 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 (phi(II)) with large transient increases in 'constitutive loss processes' (phi(NO)) prior to dissipation of excitation by non-photochemical quenching (phi(NPQ)). 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.FII and.electron transport rate using either.photosynthetically active radiation or Delta R-685 as indicators of leaf irradiance.This project was supported by an Australian Research Council (ARC) Discovery grant ‘AirLIFT’ (DP140101488) and an ARC Linkage Infrastructure, Equipment and Facilities grant (LE.0775666) and conducted in research facilities and with scientific equipment from the University of Wollongong and the Australian National University. This research was completed as part of R.W.’s PhD which was funded through an Australian Government Research Training Program Scholarship

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 aprototype light induced fluorescence transient (LIFT) device

The prototype light-induced fluorescence transient (LIFT) instrument provides continuous, minimally intrusive, high time resolution (~2 s) assessment of photosynthetic performance in terrestrial plants from up to 2 m. It induces a chlorophyll fluorescence transient by a series of short flashes in a saturation sequence (180 ~1μs flashlets in <380 μs) to achieve near-full reduction of the primary acceptor QA, followed by a relaxation sequence (RQA; 90 flashlets at exponentially increasing intervals over ~30 ms) to observe kinetics of QA re-oxidation. When fitted by the fast repetition rate (FRR) model (Kolber et al. 1998) the QA flash of LIFT/FRR gives smaller values for FmQA from dark adapted leaves than FmPAM from pulse amplitude modulated (PAM) assays. The ratio FmQA/FmPAM resembles the ratio of fluorescence yield at the J/P phases of the classical O-J-I-P transient and we conclude that the difference simply is due to the levels of PQ pool reduction induced by the two techniques. In a strong PAM-analogous WL pulse in the dark monitored by the QA flash of LIFT/FRR φPSIIWL ≈ φPSIIPAM. The QA flash also tracks PQ pool reduction as well as the associated responses of ETR QA → PQ and PQ → PSI, the relative functional (σPSII) and optical absorption (aPSII) cross-sections of PSII in situ with a time resolution of ~2 s as they relax after the pulse. It is impractical to deliver strong WL pulses at a distance in the field but a longer PQ flash from LIFT/FRR also achieves full reduction of PQ pool and delivers φPSIIPQ ≈ φPSIIPAM to obtain PAM-equivalent estimates of ETR and NPQ at a distance. In situ values of σPSII and aPSII from the QA flash with smaller antenna barley (chlorina-f2) and Arabidopsis mutants (asLhcb2–12, ch1–3 Lhcb5) are proportionally similar to those previously reported from in vitro assays. These direct measurements are further validated by changes in antenna size in response to growth irradiance. We illustrate how the QA flash facilitates our understanding of photosynthetic regulation during sun flecks in natural environments at a distance, with a time resolution of a few seconds.This research was initiated by a University of Wollongong start-up grant that facilitated the development of the LIFT instrument by Zbigniew Kolber who also advised on its set up. Australian Research Council grants DP120100872 (to the late Warwick Hillier) supported WSC and AZ, DP140101488 supported SAR and RW is in receipt of a Research Training Program scholarship

Latitudinal Biogeographic Structuring in the Globally Distributed Moss Ceratodon purpureus.

Biogeographic patterns of globally widespread species are expected to reflect regional structure, as well as connectivity caused by occasional long-distance dispersal. We assessed the level and drivers of population structure, connectivity, and timescales of population isolation in one of the most widespread and ruderal plants in the world - the common moss Ceratodon purpureus. We applied phylogenetic, population genetic, and molecular dating analyses to a global (n = 147) sampling data set, using three chloroplast loci and one nuclear locus. The plastid data revealed several distinct and geographically structured lineages, with connectivity patterns associated with worldwide, latitudinal "bands." These imply that connectivity is strongly influenced by global atmospheric circulation patterns, with dispersal and establishment beyond these latitudinal bands less common. Biogeographic patterns were less clear within the nuclear marker, with gene duplication likely hindering the detection of these. Divergence time analyses indicated that the current matrilineal population structure in C. purpureus has developed over the past six million years, with lineages diverging during the late Miocene, Pliocene, and Quaternary. Several colonization events in the Antarctic were apparent, as well as one old and distinct Antarctic clade, possibly isolated on the continent since the Pliocene. As C. purpureus is considered a model organism, the matrilineal biogeographic structure identified here provides a useful framework for future genetic and developmental studies on bryophytes. Our general findings may also be relevant to understanding global environmental influences on the biogeography of other organisms with microscopic propagules (e.g., spores) dispersed by wind.NERC PhD studentship NE/K50094X/