Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land.

Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.

Hypometabolism to survive the long polar night and subsequent successful return to light in the diatom Fragilariopsis cylindrus.

Diatoms, the main eukaryotic phytoplankton of the polar marine regions, are essential for the maintenance of food chains specific to Arctic and Antarctic ecosystems, and are experiencing major disturbances under current climate change. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their endurance during the long polar night. Here, using the polar diatom Fragilariopsis cylindrus, we report an integrative analysis combining transcriptomic, microscopic and biochemical approaches to shed light on the strategies used to survive the polar night. We reveal that in prolonged darkness, diatom cells enter a state of quiescence with reduced metabolic and transcriptional activity, during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness, including the appearance of a large vacuole. Our results further show that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis, demonstrating the remarkable robustness of polar diatoms to prolonged darkness at low temperature.

The Photoprotective Behavior of a Motile Benthic Diatom as Elucidated from the Interplay Between Cell Motility and Physiological Responses to a Light Microgradient Using a Novel Experimental Setup.

It has long been hypothesized that benthic motile pennate diatoms use phototaxis to optimize photosynthesis and minimize photoinhibitory damage by adjusting their position within vertical light gradients in coastal benthic sediments. However, experimental evidence to test this hypothesis remains inconclusive, mainly due to methodological difficulties in studying cell behavior and photosynthesis over realistic spatial microscale gradients of irradiance and cell position. In this study, a novel experimental approach was developed and used to test the hypothesis of photosynthesis optimization through motility, based on the combination of single-cell in vivo chlorophyll fluorometry and microfluidic chips. The approach allows the concurrent study of behavior and photosynthetic activity of individual cells of the epipelic diatom species Craspedostauros britannicus exposed to a light microgradient of realistic dimensions, simulating the irradiance and distance scales of light microgradients in benthic sediments. Following exposure to light, (i) cells explored their light environment before initiating light-directed motility; (ii) cells used motility to lower their light dose, when exposed to the highest light intensities; and (iii) motility was combined with reversible non-photochemical quenching, to allow cells to avoid photoinhibition. The results of this proof-of-concept study not only strongly support the photoprotective nature of photobehavior in the studied species but also revealed considerable variability in how individual cells reacted to a light microgradient. The experimental setup can be readily applied to study motility and photosynthetic light responses of other diatom species or natural assemblages, as well as other photoautotrophic motile microorganisms, broadening the toolset for experimental microbial ecology research.

Photoinhibition in optically thick samples: Effects of light attenuation on chlorophyll fluorescence-based parameters.

Oxygenic photoautotrophs are, paradoxically, subject to photoinhibition of their photosynthetic apparatus, in particular one of its major components, the Photosystem II (PSII). Photoinhibition is generalized across species, light conditions and habitats, imposing substantial metabolic costs that lower photosynthetic productivity and constrain the niches of photoautotrophy. As a process driven by light reaching PSII, light attenuation in optically thick samples influences both the actual extent, and the detection, of photoinhibition. Chlorophyll fluorescence is widely used to measure photoinhibition, but fluorescence-based parameters are affected by light attenuation of both downwelling incident radiation traversing the sample to reach PSII, and emitted fluorescence upwelling through the sample. We used modelling, experimental manipulation of within-sample light attenuation, and meta-analysis of published data, to show substantial, differential effects of light attenuation and depth-integration of emitted fluorescence upon measurements of photoinhibition. Numerical simulations and experimental manipulation of light attenuation indicated that PSII photoinactivation tracked using chlorophyll fluorescence can appear to be over three times lower than the inherent cellular susceptibility to photoinactivation, in optically-dense samples such as leaves or biofilms. The meta-analysis of published data showed that this general trend was unknowingly present in the literature, revealing an overall difference of more than five times between optically thick leaves and optically thin cell suspensions. Although fluorescence-based parameters may provide ecophysiologically relevant information for characterizing the sample as a whole, light attenuation and depth integration can vary between samples independently of their intrinsic physiology. They should be used with caution when aiming to quantify in absolute terms inherent photoinhibition-related parameters in optically thick samples.

Elemental Stoichiometry and Photophysiology Regulation of Synechococcus sp. PCC7002 Under Increasing Severity of Chronic Iron Limitation.

Iron (Fe) is an essential cofactor for many metabolic enzymes of photoautotrophs. Although Fe limits phytoplankton productivity in broad areas of the ocean, phytoplankton have adapted their metabolism and growth to survive in these conditions. Using the euryhaline cyanobacterium Synechococcus sp. PCC7002, we investigated the physiological responses to long-term acclimation to four levels of Fe availability representative of the contemporary ocean (36.7, 3.83, 0.47 and 0.047 pM Fe'). With increasing severity of Fe limitation, Synechococcus sp. cells gradually decreased their volume and growth while increasing their energy allocation into organic carbon and nitrogen cellular pools. Furthermore, the total cellular content of pigments decreased. Additionally, with increasing severity of Fe limitation, intertwined responses of PSII functional cross-section (σPSII), re-oxidation time of the plastoquinone primary acceptor QA (τ) and non-photochemical quenching revealed a shift in the photophysiological response between mild to strong Fe limitation compared with severe limitation. Under mild and strong Fe limitation, there was a decrease in linear electron transport accompanied by progressive loss of state transitions. Under severe Fe limitation, state transitions seemed to be largely supplanted by alternative electron pathways. In addition, mechanisms to dissipate energy excess and minimize oxidative stress associated with high irradiances increased with increasing severity of Fe limitation. Overall, our results establish the sequence of physiological strategies adopted by the cells under increasing severity of chronic Fe limitation, within a range of Fe concentrations relevant to modern ocean biogeochemistry.

Correction to: Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover.

In Table 2 of the original publication, all instances of krec in the Parameter and Equation columns should read krecinact.

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 (Φe,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 Φe,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.

Connectivity among Photosystem II centers in phytoplankters: Patterns and responses.

Fast Repetition and Relaxation chlorophyll fluorescence induction is used to estimate the effective absorption cross section of PSII (σPSII), to analyze phytoplankton acclimation and electron transport. The fitting coefficient ρ measures excitation transfer from closed PSII to remaining open PSII upon illumination, which could theoretically generate a progressive increase in σPSII for the remaining open PSII. To investigate how ρ responds to illumination we grew marine phytoplankters with diverse antenna structures (Prochlorococcus, Synechococcus, Ostreococcus and Thalassiosira pseudonana) under limiting or saturating growth light. Initial ρ varied with growth light in Synechococcus and Thalassiosira. With increasing actinic illumination PSII closed progressively and ρ decreased for all four taxa, in a pattern explicable as an exponential decay of ρ with increasing distance between remaining open PSII reaction centers. This light-dependent down-regulation of ρ allows the four phytoplankters to limit the effect of increasing light upon σPSII. The four structurally distinct taxa showed, however, distinct rates of response of ρ to PSII closure, likely reflecting differences in the spacing or orientation among their PSII centers. Following saturating illumination recovery of ρ in darkness coincided directly with PSII re-opening in Prochlorococcus. Even after PSII had re-opened in Synechococcus a transition to State II slowed dark recovery of ρ. In Ostreococcus sustained NPQ slowed dark recovery of ρ. In Thalassiosira dark recovery of ρ was slowed, possibly by a light-induced change in PSII spacing. These patterns of ρ versus PSII closure are thus a convenient probe of comparative PSII spacings.

Interactive effects of nitrogen and light on growth rates and RUBISCO content of small and large centric diatoms.

Among marine phytoplankton groups, diatoms span the widest range of cell size, with resulting effects upon their nitrogen uptake, photosynthesis and growth responses to light. We grew two strains of marine centric diatoms differing by ~4 orders of magnitude in cell biovolume in high (enriched artificial seawater with ~500 µmol L-1 µmol L-1 NO3-) and lower-nitrogen (enriched artificial seawater with <10 µmol L-1 NO3-) media, across a range of growth light levels. Nitrogen and total protein per cell decreased with increasing growth light in both species when grown under the lower-nitrogen media. Cells growing under lower-nitrogen media increased their cellular allocation to RUBISCO and their rate of electron transport away from PSII, for the smaller diatom under low growth light and for the larger diatom across the range of growth lights. The smaller coastal diatom Thalassiosira pseudonana is able to exploit high nitrogen in growth media by up-regulating growth rate, but the same high-nitrogen growth media inhibits growth of the larger diatom species.

Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover.

Micromonas strains of small prasinophyte green algae are found throughout the world's oceans, exploiting widely different niches. We grew arctic and temperate strains of Micromonas and compared their susceptibilities to photoinactivation of Photosystem II, their counteracting Photosystem II repair capacities, their Photosystem II content, and their induction and relaxation of non-photochemical quenching. In the arctic strain Micromonas NCMA 2099, the cellular content of active Photosystem II represents only about 50 % of total Photosystem II protein, as a slow rate constant for clearance of PsbA protein limits instantaneous repair. In contrast, the temperate strain NCMA 1646 shows a faster clearance of PsbA protein which allows it to maintain active Photosystem II content equivalent to total Photosystem II protein. Under growth at 2 °C, the arctic Micromonas maintains a constitutive induction of xanthophyll deepoxidation, shown by second-derivative whole-cell spectra, which supports strong induction of non-photochemical quenching under low to moderate light, even if xanthophyll cycling is blocked. This non-photochemical quenching, however, relaxes during subsequent darkness with kinetics nearly comparable to the temperate Micromonas NCMA 1646, thereby limiting the opportunity cost of sustained downregulation of PSII function after a decrease in light.

Diatom growth responses to photoperiod and light are predictable from diel reductant generation.

Light drives phytoplankton productivity, so phytoplankton must exploit variable intensities and durations of light exposure, depending upon season, latitude, and depth. We analyzed the growth, photophysiology and composition of small, Thalassiosira pseudonana, and large, Thalassiosira punctigera, centric diatoms from temperate, coastal marine habitats, responding to a matrix of photoperiods and growth light intensities. T. pseudonana showed fastest growth rates under long photoperiods and low to moderate light intensities, while the larger T. punctigera showed fastest growth rates under short photoperiods and higher light intensities. Photosystem II function and content responded primarily to instantaneous growth light intensities during the photoperiod, while diel carbon fixation and RUBISCO content responded more to photoperiod duration than to instantaneous light intensity. Changing photoperiods caused species-specific changes in the responses of photochemical yield (e- /photon) to growth light intensity. These photophysiological variables showed complex responses to photoperiod and to growth light intensity. Growth rate also showed complex responses to photoperiod and growth light intensity. But these complex responses resolved into a close relation between growth rate and the cumulative daily generation of reductant, across the matrix of photoperiods and light intensities.

Photosystem II repair in marine diatoms with contrasting photophysiologies.

Skeletonema costatum and Phaeodactylum tricornutum are model marine diatoms with differing strategies for non-photochemical dissipation of excess excitation energy within photosystem II (PSII). We showed that S. costatum, with connectivity across the pigment bed serving PSII, and limited capacity for induction of sustained non-photochemical quenching (NPQ), maintained a large ratio of [PSII(Total)]/[PSII(Active)] to buffer against fluctuations in light intensity. In contrast, P. tricornutum, with a larger capacity to induce sustained NPQ, could maintain a lower [PSII(Total)]/[PSII(Active)]. Induction of NPQ was correlated with an active PSII repair cycle in both species, and inhibition of chloroplastic protein synthesis with lincomycin leads to run away over-excitation of remaining PSII(Active), particularly in S. costatum. We discuss these distinctions in relation to the differing capacities, induction and relaxation rates for NPQ, and as strain adaptations to the differential light regimes of their originating habitats. The present work further confirms the important role for the light-dependent fast regulation of photochemistry by NPQ interacting with PSII repair cycle capacity in the ecophysiology of both pennate and centric diatoms.

The nitrogen costs of photosynthesis in a diatom under current and future pCO2.

With each cellular generation, oxygenic photoautotrophs must accumulate abundant protein complexes that mediate light capture, photosynthetic electron transport and carbon fixation. In addition to this net synthesis, oxygenic photoautotrophs must counter the light-dependent photoinactivation of Photosystem II (PSII), using metabolically expensive proteolysis, disassembly, resynthesis and re-assembly of protein subunits. We used growth rates, elemental analyses and protein quantitations to estimate the nitrogen (N) metabolism costs to both accumulate the photosynthetic system and to maintain PSII function in the diatom Thalassiosira pseudonana, growing at two pCO2 levels across a range of light levels. The photosynthetic system contains c. 15-25% of total cellular N. Under low growth light, N (re)cycling through PSII repair is only c. 1% of the cellular N assimilation rate. As growth light increases to inhibitory levels, N metabolite cycling through PSII repair increases to c. 14% of the cellular N assimilation rate. Cells growing under the assumed future 750 ppmv pCO2 show higher growth rates under optimal light, coinciding with a lowered N metabolic cost to maintain photosynthesis, but then suffer greater photoinhibition of growth under excess light, coincident with rising costs to maintain photosynthesis. We predict this quantitative trait response to light will vary across taxa.

Electron transport kinetics in the diazotrophic cyanobacterium Trichodesmium spp. grown across a range of light levels.

The diazotrophic cyanobacterium Trichodesmium is a major contributor to marine nitrogen fixation. We analyzed how light acclimation influences the photophysiological performance of Trichodesmium IMS101 during exponential growth in semi-continuous nitrogen fixing cultures under light levels of 70, 150, 250, and 400 µmol photons m(-2) s(-1), across diel cycles. There were close correlations between growth rate, trichome length, particulate organic carbon and nitrogen assimilation, and cellular absorbance, which all peaked at 150 µmol photons m(-2) s(-1). Growth rate was light saturated by about 100 µmol photons m(-2) s(-1) and was photoinhibited above 150 µmol photons m(-2) s(-1). In contrast, the light level (I k) to saturate PSII electron transport (e (-) PSII(-1) s(-1)) was much higher, in the range of 450-550 µmol photons m(-2) s(-1), and increased with growth light. Growth rate correlates with the absorption cross section as well as with absorbed photons per cell, but not to electron transport per PSII; this disparity suggests that numbers of PSII in a cell, along with the energy allocation between two photosystems and the state transition mechanism underlie the changes in growth rates. The rate of state transitions after a transfer to darkness increased with growth light, indicating faster respiratory input into the intersystem electron transport chain.

Changes in the Rubisco to photosystem ratio dominates photoacclimation across phytoplankton taxa.

When growth irradiance changes, phytoplankton acclimates by changing allocations to cellular components to re-balance their capacity to absorb photons versus their capacity to use the electrons from the oxidation of water at photosystem II. Published changes in the cellular allocations resulting from photoacclimation across algal groups highlight that algae adopt different strategies. We examined the photoacclimation of the photosynthetic apparatus of six marine phytoplankters under near-natural diel irradiance patterns. For most of the phytoplankters, Chl a per structural photosystem II unit decreased with increasing growth irradiance, but a parallel decline in optical packaging effect allowed cells to maintain their functional absorption cross section serving active photosystem II units (σ PSII). Furthermore, no significant changes were observed in the ratio of Chl a per photosystem I. The diatom Skeletonema marinoi proved an exception to this pattern as Chl a per photosystem II is stable and Chl a per photosystem I slightly decreased with light intensity. A clear decrease in the photosystem content per cell was observed for all species except for Thalassiosira oceanica and S. marinoi. Rubisco content per cell showed little variation with irradiance for most algae, except for a 3-fold increase in S. marinoi. A ~700 % increase in the Rubisco:photosystem ratio across species with increasing growth irradiance indicates this is a key cellular stoichiometric adjustment to balance photon absorption capacity and the carbon reduction capacity. Increasing the Rubisco:photosystem ratio occurs through a decrease in the photosystems per cell for most of the phytoplankters in this study, except in the case of S. marinoi where Rubisco per cell increased.

Ocean acidification alters the photosynthetic responses of a coccolithophorid to fluctuating ultraviolet and visible radiation.

Mixing of seawater subjects phytoplankton to fluctuations in photosynthetically active radiation (400-700 nm) and ultraviolet radiation (UVR; 280-400 nm). These irradiance fluctuations are now superimposed upon ocean acidification and thinning of the upper mixing layer through stratification, which alters mixing regimes. Therefore, we examined the photosynthetic carbon fixation and photochemical performance of a coccolithophore, Gephyrocapsa oceanica, grown under high, future (1,000 µatm) and low, current (390 µatm) CO2 levels, under regimes of fluctuating irradiances with or without UVR. Under both CO2 levels, fluctuating irradiances, as compared with constant irradiance, led to lower nonphotochemical quenching and less UVR-induced inhibition of carbon fixation and photosystem II electron transport. The cells grown under high CO2 showed a lower photosynthetic carbon fixation rate but lower nonphotochemical quenching and less ultraviolet B (280-315 nm)-induced inhibition. Ultraviolet A (315-400 nm) led to less enhancement of the photosynthetic carbon fixation in the high-CO2-grown cells under fluctuating irradiance. Our data suggest that ocean acidification and fast mixing or fluctuation of solar radiation will act synergistically to lower carbon fixation by G. oceanica, although ocean acidification may decrease ultraviolet B-related photochemical inhibition.

CyanoCyc cyanobacterial web portal.

CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists' work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.

Parameterization of photosystem II photoinactivation and repair.

The photoinactivation (also termed photoinhibition or photodamage) of Photosystem II (PSII) and the counteracting repair reactions are fundamental elements of the metabolism and ecophysiology of oxygenic photoautotrophs. Differences in the quantification, parameterization and terminology of Photosystem II photoinactivation and repair can erect barriers to understanding, and particular parameterizations are sometimes incorrectly associated with particular mechanistic models. These issues lead to problems for ecophysiologists seeking robust methods to include photoinhibition in ecological models. We present a comparative analysis of terms and parameterizations applied to photoinactivation and repair of Photosystem II. In particular, we show that the target size and quantum yield approaches are interconvertible generalizations of the rate constant of photoinactivation across a range of incident light levels. Our particular emphasis is on phytoplankton, although we draw upon the literature from vascular plants. This article is part of a Special Issue entitled: Photosystem II.

Photosystem II photoinactivation, repair, and protection in marine centric diatoms.

Diatoms are important contributors to aquatic primary production, and can dominate phytoplankton communities under variable light regimes. We grew two marine diatoms, the small Thalassiosira pseudonana and the large Coscinodiscus radiatus, across a range of temperatures and treated them with a light challenge to understand their exploitation of variable light environments. In the smaller T. pseudonana, photosystem II (PSII) photoinactivation outran the clearance of PSII protein subunits, particularly in cells grown at sub- or supraoptimal temperatures. In turn the absorption cross section serving PSII photochemistry was down-regulated in T. pseudonana through induction of a sustained phase of nonphotochemical quenching that relaxed only slowly over 30 min of subsequent low-light incubation. In contrast, in the larger diatom C. radiatus, PSII subunit turnover was sufficient to counteract a lower intrinsic susceptibility to photoinactivation, and C. radiatus thus did not need to induce sustained nonphotochemical quenching under the high-light treatment. T. pseudonana thus incurs an opportunity cost of sustained photosynthetic down-regulation after the end of an upward light shift, whereas the larger C. radiatus can maintain a balanced PSII repair cycle under comparable conditions.

Increased reliance upon photosystem II repair following acclimation to high-light by coral-dinoflagellate symbioses.

Changing light environments force photoautotroph cells, including coral symbionts, to acclimate to maintain photosynthesis. Photosystem II (PSII) is subjected to photoinactivation at a rate proportional to the incident light, and cells must adjust their rates of protein repair to counter this photoinactivation. We examined PSII function in the coral symbiont Symbiodinium to determine the effect of photoacclimation on their capacity for PSII repair. Colonies of the coral Stylophora pistillata were collected from moderate light environments on the Lizard Island reef (Queensland, Australia) and transported to a local field station, where they were assigned to lower or higher light regimes and allowed to acclimate for 2 weeks. Following this photoacclimation period, the low-light acclimated corals showed greater symbiont density, higher chlorophyll per symbiont cell, and higher photosystem II protein than high-light acclimated corals did. Subsequently, we treated the corals with lincomycin, an inhibitor of chloroplastic protein synthesis, and exposed them to a high-light treatment to separate the effect of de novo protein synthesis in PSII repair from intrinsic susceptibility to photoinactivation. Low-light acclimated corals showed a sharp initial drop in PSII function but inhibition of PSII repair provoked only a modest additional drop in PSII function, compared to uninhibited corals. In high-light acclimated corals inhibition of PSII repair provoked a larger drop in PSII function, compared to uninhibited high-light corals. The greater lincomycin effects in the corals pre-acclimated to high-light show that high-light leads to an increased reliance on the PSII repair cycle.