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Photosynthesis in the seagrass Zostera muelleri remains poorly understood. We investigated the effect of reduced irradiance on the incorporation of 13C, gene expression of photosynthetic, photorespiratory and intermediates recycling genes as well as the enzymatic content and activity of Rubisco and PEPC within Z. muelleri. Following 48 h of reduced irradiance, we found that i) there was a ∼7 fold reduction in 13C incorporation in above ground tissue, ii) a significant down regulation of photosynthetic, photorespiratory and intermediates recycling genes and iii) no significant difference in enzyme activity and content. We propose that Z. muelleri is able to alter its physiology in order to reduce the amount of C lost through photorespiration to compensate for the reduced carbon assimilation as a result of reduced irradiance. In addition, the first estimated rate constant (Kcat) and maximum rates of carboxylation (Vcmax) of Rubisco is reported for the first time for Z. muelleri.

Rhodopsin transmembrane proton pumps (fuelled by visible light which is absorbed by retinal (carotenoid) chromophores) exist in all three domains of living species and in all groups of true fungi studied. Light driven proton and sodium pumps are likely to be essential for some marine fungi, especially hypersaline tolerant and endolithic species. Rhodopsin macromolecular machines, using visible light, drive metabolic reactions in addition to those provided by aerobic respiration, providing extra energy needed for the maintenance and growth of fungi, especially in euphotic environments where oxygen concentration is limited. In addition, dissimilatory nitrate and metal oxide reduction can provide sources of energy for fungi in the absence of oxygen, for example, in fungal species growing in marine sediments. Finally, the oxidation of elemental sulphur, iron and manganese can be a source of energy. Some fungi are, therefore, lithotrophs and photoheterotrophs. The ecological implications of these latter processes are discussed.

The isoetid life-form was originally defined on morphological grounds; subsequent physiological investigations showed that all of the isoetids examined took up a large fraction of the inorganic C fixed in their leaves from the root medium under natural conditions, and that some of them carried out much of their assimilation of inorganic C via a CAM-like mechanism. Root-dominated uptake of inorganic C appeared to be unique to, and ubiquitous in, the isoetids. I However, a large capacity for CAM-like metabolism in submerged vascular plants is not universal in isoetids, nor is it restricted to this life-form, being also found in Crassulaa aquatica. The work described here shows that submerged specimens of the North American Eriocaulon decangulare have a high fraction of their dry weight in the root system, a trait characteristic of isoetids but uncommon in other submerged vascular plants. E. decangulare has vesicular-arbuscular mycorrhizas, as do other flowering plant isoetids hut not, generally, submerged Isoetes spp. Under conditions of natural supply of inorganic C, E. decangulare, like other isoetids, takes up most of its inorganic C through its roots. Uptake of inorganic C by both roots and shoots involves CO

An analysis of published data suggests that the N

Summary The benefits which this paper addresses are those of maintaining the intracellular acid-base balance during growth, and of generating osmolarity related to regulation of turgor in environments of low water potential. These benefits may incur costs in terms of the quantity of potentially growth-limiting resources (photons, water, nitrogen) which are needed to produce unit quantity of ‘baseline’ plant biomass. The direction (excess H+ or excess OH−) and magnitude of acid–base perturbation during growth depends on the nature of the N-source (NH4+, N2 or NO3−), so that the costing of pH homoiostasis involves consideration of the costs of overall N-assimilation for comparison with the other costs of growth of a terrestrial C3 plant. Photon costs for the various biochemical and transport processes involved in overall growth, N-assimilation, pH regulation and osmolarity generation are computed using known stoichiometries of coupled reactions. Water costs are deduced from the C-requirements for the various processes (including C lost in associated decarboxylations) by assuming a constant value of water lost in transpiration per unit net C fixed in an illuminated shoot. Nitrogen costs are deduced from the N-content of the plants or compounds under consideration. The computed costs for N-assimilation and the generation of osmolarity are referred to the costs of ‘baseline’ plant synthesis using the cheapest mechanisms (NH4+ as source for N-assimilation; inorganic ions as the basis for osmolarity generation) so that the increment of cost related to assimilation of N2or NO3−, or of osmolarity generation using an organic compatible solute, can be presented. Photon costs of growth with N2 fixation and the processes associated with regulation of pH are (granted the assumptions made as to stoichiometries and plant composition) 9 % higher than are those of growth with NH4+ as N˜ source. The predicted cost of growth with NO3− as N source depends on the location of NO3− reduction and the mechanism of OH− disposal, and ranges from 5 to 12% more than that for growth with NH4+ as N source. H2O (transpiration) costs follow a similar pattern, with growth on N2 as N source costing 12% more, and growth on NO3− costing to 1–2 to 167 % more, than growth with NH4+ as N source. The extra costs in photons of using compatible solutes (sorbitol, proline or glycine betaine) to generate an osmolarity of 500 osmol m−3 in all of the non-apoplastic water of the plant add 21·5 to 26·1 % to the total costs of growth, while use of compatible solutes to generate osmolarity in ‘N’ phases (i.e. cytosol, plastid stroma, mitochondrial matrix) alone would add 5·2 to 6·2% The costs of growth in terms of transpirational water are increased 7·9 to 98 % by the use of compatible solutes for osmolarity generation in the ‘N’ phases only. The increments for the N-containing solutes are higher when NO3− is the N-source rather than NH4+. The N-cost of growth with N-containing compatible solutes generating 500 osmol m−3 in ‘N’ phases increases the N cost of growth by 33%. These predicted costs are under-estimates of ‘real’ costs which take into account the occurrence of alternate oxidase activity under some growth conditions and the production of additional organic acid anions with N2 as opposed to NH4+ as N source. Nevertheless, the predicted minimum costs of attaining the benefits of pH regulation and of turgor generation are of use in suggesting where selectively significant (i.e. low requirement for a scarce resource) alternative mechanisms may occur. Examples include a possible photon saving by using NH4+ rather than N2 or NO3− where all three are available; a possible water saving by use of photoreduction of NO3− in leaves in arid environments; and a possible N saving by use of non-N-containing compatible solutes (polyols) in environments of low water potential. Proof of these suggestions involves comparisons of inclusive fitness of genotypes possessing the trait under consideration with that of genotypes lacking the trait.

SUMMARY This paper relates the 13C/12C ratio of C3 plant material relative to that of source CO2 to the N source for growth, the organic N content of the plant, and the extent of organic acid synthesis. The 13C/12C ratio is quantified as Δ, defined as (δ13C substrate –δ13C product)/(1+δ13C product), where δ13C values of substrate or product (i.e. the samples) are defined as [13C/12C]sample]/[(13C/12C)standard]−1. The computation is performed by relating differences in plant composition as a function of N nutrition and acid synthesis to the fraction of plant C which is acquired via Rubisco and via other carboxylases. The fractional contribution of the different carboxylases to C gain is then related, using the known isotopic fractionations exhibited by these carboxylases, in a model to predict the final Δ of the plant (relative to atmospheric CO2). Application of this approach to a ‘typical’ C3 land plant yields predictions of the decrease of Δ relative to a hypothetical case in which all C is fixed via Rubisco. The predicted decreases range from 0–24 %, for NH4+ assimilation (which always occurs in the roots) to 2–80%, for NO3− assimilation in shoots with the organic acid salt which results from acid-base balance, plus any additional organic acid salts plus free acids for a plant with a basal C:N molar ratio in organic material of 15. Intermediate values are predicted for symbiotic growth with N2, or where NO3− assimilation in root or shoot is accompanied by some acid-base regulation via OH- loss to the root medium. Comparison with published data on the difference in Δ of Ricinus communis cultured with NH4+ or NO3− shows that the measured influence of nitrogen source is in the right direction (NO3− grown plants with a smaller Δ, i.e. a larger deviation from the value predicted for the absence of non-Rubisco carboxylations) to be explained by the observed difference in composition and hence fractional C contribution by the various carboxylases. However, the effect of N source on Δ is greater than that predicted by the model, i.e. a 2.1 % decrease as opposed to a 0.10 % decrease. It is likely that the major cause of the difference in δ13C of the plants grown on the two N sources is a change in the ratio of transport and biochemical conductances of leaf photosynthesis. Such a change is quantitatively consistent with the lower water use efficiency of NH4+ -grown plants. The predicted, and observed, changes in Δ as a function of N source are of the same magnitude as those found for C3 terrestrial species grown at different temperatures or photon flux densities, or in environments yielding different water use efficiencies by changing root water supply relative to shoot evaporation potential. Variations in N source should be added to the factors which might alter δ of plants growing in the field.

Summary Fossil evidence shows that stomata have occurred in sporophytes and (briefly) gametophytes of embryophytes during the last 400 m yr. Cladistic analyses with hornworts basal are consistent with a unique origin of stomata, although cladograms with hornworts as the deepest branching embryophytes require loss of stomata early in the evolution of liverworts. Functional considerations suggest that stomata evolved from pores in the epidermis of plant organs which were at least three cell layers thick and had intercellular gas spaces and a cuticle; an endohydric conducting system would not have been necessary for low-growing rhizophytes, especially in early Palaeozoic CO2-rich atmospheres. The ‘prestomatal state’ (pores) would have permitted higher photosynthetic rates per unit ground area. Functional stomata, and endohydry, permit the evolution of homoiohydry and the loss of vegetative desiccation tolerance and plants > 1 m tall. Stomatal functioning would then have involved maintenance of hydration, and restricting the occurrence of xylem embolism, under relatively desiccating conditions at the expense of limiting carbon acquisition. The time scale of environmental fluctuations over which stomatal responses can maximize carbon gain per unit water loss varies among taxa and life forms.

The earliest branching cyanobacterium, Gloeobacter, exhibits a number of ancestral traits including the lack of thylakoids. It occurs epilithically in microbial mats, both subaerially and submerged...

Many phytoplankton organisms are denser than their aquatic medium, and so sink relative to the surrounding water. Decreasing cell density relative to the medium allows upward movement, using gas vesicles in cyanobacteria and decreasing the density of the vacuole in large-celled eukaryotes. Upward movement can also occur in organisms with flagella. These three mechanisms can maintain the organisms in the photic zone with a small estimated minimum energy cost relative to those of cell growth (

Protein assemblages in the plasma membrane of photosynthetic organisms include the polar occurrence of PIN proteins permitting polar auxin transport in embryophytes and Charales, and the H+ ATPase in acid zones of Charales cells. Production of small radius of curvature membrane areas in transfer cells and charasomes is incompletely understood.

The literature, and previously unpublished data from the authors’ laboratories, shows that the δ13C of organic matter in marine macroalgae and seagrasses collected from the natural environment ranges from –3 to –35‰. While some marine macroalgae have δ13C values ranging over more than 10‰ within the thallus of an individual (some brown macroalgae), in other cases the range within a species collected over a very wide geographical range is only 5‰ (e.g. the red alga Plocamium cartilagineum which has values between –30 and –35‰). The organisms with very negative δ13C (lower than –30‰) are mainly subtidal red algae, with some intertidal red algae and a few green algae; those with very positive δ13C values (higher than –10‰) are mainly green macroalgae and seagrasses, with some red and brown macroalgae. The δ13C value correlates primarily with taxonomy and secondarily with ecology. None of the organisms with δ13C values lower than –30‰ have pyrenoids. Previous work showed a good correlation between δ13C values lower than –30‰ and the lack of CO2 concentrating mechanisms for several species of marine red algae. The extent to which the low δ13C values are confined to organisms with diffusive CO2 entry is discussed. Diffusive CO2 entry could also occur in organisms with higher δ13C values if diffusive conductance was relatively low. The photosynthesis of organisms with δ13C values more positive than –10‰ (i.e. more positive than the δ13C of CO2 in seawater) must involve HCO3- use.

Inorganic carbon assimilation in algae depends ultimately on the activity of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) and the Calvin-Benson-Bassham Cycle (Photosynthetic Carbon Reduction Cycle; PCRC). The kinetic characteristics of the different forms of Rubisco found in algae and cyanobacteria are such that under present day levels of CO2 and oxygen, inefficiencies in carbon assimilation, involving, inter alia, photorespiration would occur. Given this, achievement of significant rates of net photosynthesis necessitates the operation of CO2 concentrating mechanisms (CCMs) to elevate CO2 concentrations, and increase CO2:O2 ratios at the active site of Rubisco. The biochemical, C4 photosynthesis, CCM appears to be limited to the marine ulvophycean alga Udotea flabellum and one species of a marine diatom (Thalassiosira weisflogii) as well as in some seagrasses and freshwater macrophytes. With few exceptions all other algae and the cyanobacteria possess a biophysical CCM, based on active transport of inorganic carbon. Despite many years of research into CCMs, there is still a good deal of misunderstanding about what comprises reliable and robust evidence for CCM activity. By definition, there needs to be a demonstrable net positive gradient of CO2 in > CO2 out. In addition, cells with active CCMs have K0.5CO2 values for DIC-dependent photosynthesis less than that for their Rubiscos. Other features such as isotope discrimination can also be useful, with cells using CO2 diffusion alone showing ∆13C values ~ −30‰ and discrimination values becoming less negative as CCM activity increases. However, the presence of gene sequences for, or even expressed activity of, enzymes such as PEP carboxylase, are not good indicators of operation of C4 photosynthesis. It is a common misconception that possession of external carbonic anhydrase can alone result in CO2 accumulation. CCMs involve active transport of bicarbonate and/or CO2. In cyanobacteria this occurs at the thylakoid membrane or plasmalemma and in eukaryotes at the plasmalemma or inner plastid envelope, or both. CCMs in cyanobacteria also involve polyhedral protein-walled bodies termed carboxysomes it is here that the bulk of Rubisco is found and CO2 is accumulated due to the activity of carbonic anhydrase. The analogous structure found in some eukaryotes is the pyrenoid (Chap. 9). All pyrenoid-containing algae have CCMs but not all algae with CCMs have pyrenoids. Though work on eukaryotic algae has, so far, lagged behind that in cyanobacteria new advances in molecular biology have led to identification of many of the proteins, and elucidation of the mechanisms, involved in inorganic carbon acquisition.

Cell size influences the rate at which phytoplankton assimilate dissolved inorganic carbon (DIC), but it is unclear whether volume-specific carbon uptake should be greater in smaller or larger cells. On the one hand, Fick's Law predicts smaller cells to have a superior diffusive CO2 supply. On the other, larger cells may have greater scope to invest metabolic energy to upregulate active transport per unit area through CO2 -concentrating mechanisms (CCMs). Previous studies have focused on among-species comparisons, which complicates disentangling the role of cell size from other covarying traits. In this study, we investigated the DIC assimilation of the green alga Dunaliella tertiolecta after using artificial selection to evolve a 9.3-fold difference in cell volume. We compared CO2 affinity, external carbonic anhydrase (CAext ), isotopic signatures (δ13 C) and growth among size-selected lineages. Evolving cells to larger sizes led to an upregulation of CCMs that improved the DIC uptake of this species, with higher CO2 affinity, higher CAext and higher δ13 C. Larger cells also achieved faster growth and higher maximum biovolume densities. We showed that evolutionary shifts in cell size can alter the efficiency of DIC uptake systems to influence the fitness of a phytoplankton species.

Cl- has long been known as a micronutrient for oxygenic photosynthetic resulting from its role an essential cofactor for photosystem II (PSII). Evidence on the in vivo Cl- distribution in Spinacia oleracea leaves and chloroplasts shows that sufficient Cl- is present for the involvement in PSII function, as indicated by in vitro studies on, among other organisms, S. oleracea PsII. There is also sufficient Cl- to function, with K+ , in parsing the H+ electrochemical potential difference (proton motive force) across the illuminated thylakoid membrane into electrical potential difference and pH difference components. However, recent in vitro work on PSII from S. oleracea shows that oxygen evolving complex (OEC) synthesis, and resynthesis after photodamage, requires significantly higher Cl- concentrations than would satisfy the function of assembled PSII O2 evolution of the synthesised PSII with the OEC. The low Cl- affinity of OEC (re-)assembly could be a component limiting the rate of OEC (re-)assembly.

Oxygen uptake in illuminated photosynthetic algae can be measured using 18O2 or (with some reservations) photosystem II electron flux measured by fluorescence corrected for electron flux to sinks other than O2. Water-water cycles, involve photosystem II removing electrons from water to produce O2. Water-water cycles involving photosystem I as well as photosystem II use the Mehler-peroxidase reaction, or flavodiiron protein, in the O2 reduction reactions, with pumping of 3 H+ per electron. The other known water-water cycle involves only photosystem II, with the plastid (plastoquinol) terminal oxidase transferring electrons to O2, pumping of 1 H+ per electron. Return flux of the pumped H+ through the CFOCF1 ATP synthase can supplement or replace ATP from cyclic electron flow and oxidative phosphorylation in equating the supply of NADPH and ATP to the metabolic need. A further light-dependent O2 process in algae is the energy-consuming process of photorespiration metabolising 2-phosphoglycolate from Rubisco oxygenase activity. The rate of photorespiration relative to that of photosynthesis depends on the CO2:O2 selectivity of Rubisco, and the steady-state CO2:O2 ratio at the site of Rubisco. In most algae a CO2 concentrating mechanism limits photorespiration by increasing the CO2:O2 ratio at the site of Rubisco, though, in cyanobacteria at least, some photorespiratory flux is essential. The minimum rate of mitochondrial respiration in the light is set by the requirement in biosynthesis of carbon skeletons produced only in the tricarboxylic acid cycle; higher rates may occur to supply ATP. There are problems in allocating O2 uptake in the light among the various pathways; the use of inhibitors, mutants or knockouts of a particular pathway is undermined by the possibility, or even likelihood, of compensatory reactions.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the Calvin cycle are the dominant features of inorganic carbon assimilation in all cyanobacteria and microalgae. Rubisco carboxylase shows a relatively low affinity for CO2 and also has an oxygenase activity. These features can lead to inefficiencies in carbon assimilation, involving the process of photorespiration. However, cyanobacteria and algae possess mechanisms that minimise the effects of unfavourable Rubisco kinetics and photorespiration. These involve evolution of Rubiscos with kinetics that are more favourable to carboxylase activity and/or the presence of mechanisms that increase the concentration of CO2 at the active site of Rubisco (CO2 concentrating mechanisms, CCMs). CCMs are mostly based on active transport of HCO3. In one species of marine diatom, there appears to be a biochemical CCM where single cells show a C3–C4 intermediate form of C assimilation. In cyanobacteria HCO3− accumulation involves active transport of HCO3− at the plasmalemma and/or downhill CO2 entry with energised conversion of CO2 to HCO3− at the thylakoid membrane, with CO2 accumulated within carboxysomes that contain all of the cellular Rubisco as well as carbonic anhydrase. In eukaryotic microalgae active HCO3− transport occurs at either the plasmalemma or chloroplast envelope or both. In those algae that possess them, CO2 is ultimately concentrated within Rubisco-containing pyrenoids, though it is important to note that the presence of pyrenoids is not an absolute requirement for CCMs. Algae and cyanobacteria can assimilate inorganic carbon in the dark, a process reflecting the need of cells to replenish the supply of C4 intermediates of the TCA cycle as they are removed for biosynthesis. A few can also assimilate organic carbon sources, including in some cases by phagotrophy.

Atmospheric carbon dioxide concentration ([CO2]) increased from around 280 ppm in 1750 to 400 ppm in 2016 and is likely to continue to increase throughout this century. It has been argued that wheat, Arabidopsis, and C3 plants in general respond more positively to elevated atmospheric [CO2] under ammonium (NH4+) nutrition than under nitrate (NO3-) nutrition because elevated CO2 inhibits their photoreduction of NO3- and hence reduces their total plant nitrogen (N) assimilation and ultimately growth. Here, it is argued that the weight of evidence in the literature indicates that elevated atmospheric [CO2] does not inhibit NO3- assimilation and growth of C3 vascular plants. New data for common bean and wheat support this view and indicate that the effects of elevated atmospheric [CO2] on N assimilation and growth of C3 vascular plants will be similar regardless of the form of N assimilated.

Bloom et al. proposed that rising atmospheric CO

Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO2 availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long-standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms.

P.I.M. and C.E.L. were supported by an Australian Research Council Linkage Project (LP160100242). C.M.D. was supported by baseline funding from King Abdullah University of Science and Technology. T.K. and K.W. were supported by JSPS KAKENHI (18H04156) and the Environment Research and Technology Development Fund (S-14) of the Ministry of the Environment, Japan. B.D.E. was supported by Australian Research Council grants DP160100248 and LP150100519. D.A.S. was supported by the UK Natural Environment Research Council (NE/K008439/1), and D.K.J. was supported by the CARMA project (8021-00222B), funded by the Independent Research Fund Denmark. Funding was provided to P.M. by the Generalitat de Catalunya (MERS, 2017SGR 1588) and an Australian Research Council LIEF Project (LE170100219). This work is contributing to the ICTA ‘Unit of Excellence’ (MinECo, MDM2015-0552). O.S. was supported by an ARC DECRA (DE170101524). N.M. was supported by the Spanish Ministry of Economy, Industry and Competitiveness (MedShift project). N.B. was supported by the UK Research Councils under Natural Environment Research Council award NE/N013573/1. J.W.F. was supported by the US National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Grant No. DEB-1237517. R.S. had the support of FCT, project FCT UID/MAR/00350/2018. I.E.H. was supported by Ramon y Cajal Fellowship RYC2014-14970, co-funded by the Conselleria d’Innovacio, Recerca i Turisme of the Balearic Government and the Spanish Ministry of Economy, Industry and Competitiveness. The University of Dundee is a registered Scottish charity, no. 015096. J.P.M. was supported by the Smithsonian Institution and the National Science Foundation Long-Term Research in Environmental Biology Program (DEB-0950080, DEB-1457100, DEB-1557009).

This study describes the impacts of inorganic carbon limitation on the photosynthetic efficiency and operation of photosynthetic electron transport pathways in the biofuel-candidate microalga Nannochloropsis oculata. Using a combination of highly-controlled cultivation setup (photobioreactor), variable chlorophyll a fluorescence and transient spectroscopy methods (electrochromic shift (ECS) and P700 redox kinetics), we showed that net photosynthesis and effective quantum yield of Photosystem II (PSII) decreased in N. oculata under carbon limitation. This was accompanied by a transient increase in total proton motive force and energy-dependent non-photochemical quenching as well as slightly elevated respiration. On the other hand, under carbon limitation the rapid increase in proton motive force (PMF, estimated from the total ECS signal) was also accompanied by reduced conductivity of ATP synthase to protons (estimated from the rate of ECS decay in dark after actinic illumination). This indicates that the slow operation of ATP synthase results in the transient build-up of PMF, which leads to the activation of fast energy dissipation mechanisms such as energy-dependent non-photochemical quenching. N. oculata also increased content of lipids under carbon limitation, which compensated for reduced NAPDH consumption during decreased CO2 fixation. The integrated knowledge of the underlying energetic regulation of photosynthetic processes attained with a combination of biophysical methods may be used to identify photo-physiological signatures of the onset of carbon limitation in microalgal cultivation systems, as well as to potentially identify microalgal strains that can better acclimate to carbon limitation.

Pigments absorbing 350–1,050 nm radiation have had an important role on the Earth for at least 3.5 billion years. The ion pumping rhodopsins absorb blue and green photons using retinal and pump ions across cell membranes. Bacteriochlorophylls (BChl), absorbing in the violet/blue and near infra red (NIR), power anoxygenic photosynthesis, with one photoreaction centre; and chlorophylls (Chl), absorbing in the violet/blue and red (occasionally NIR) power oxygenic photosynthesis, with two photoreaction centres. The accessory (bacterio)chlorophylls add to the spectral range (bandwidth) of photon absorption, e.g., in algae living at depth in clear oceanic water and in algae and photosynthetic (PS) bacteria in microbial mats. Organism size, via the package effect, determines the photon absorption benefit of the costs of synthesis of the pigment–protein complexes. There are unresolved issues as to the evolution of Chls vs. BChls and the role of violet/blue and NIR radiation in PS bacteria.

Anthropogenic inputs are increasing the CO2 content of the atmosphere, and the CO2 and total inorganic C in the surface ocean and, to a lesser degree, the deep ocean. The greenhouse effect of the i...

Seagrasses are unique angiosperms that carry out growth and reproduction submerged in seawater. They occur in at least three families of the Alismatales. All have chloroplasts mainly in the cells of the epidermis. Living in seawater, the supply of inorganic carbon (Ci) to the chloroplasts is diffusion limited, especially under unstirred conditions. Therefore, the supply of CO2 and bicarbonate across the diffusive boundary layer on the outer side of the epidermis is often a limiting factor. Here we discuss the evidence for mechanisms that enhance the uptake of Ci into the epidermal cells. Since bicarbonate is plentiful in seawater, a bicarbonate pump might be expected; however, the evidence for such a pump is not strongly supported. There is evidence for a carbonic anhydrase outside the outer plasmalemma. This, together with evidence for an outward proton pump, suggests the possibility that local acidification leads to enhanced concentrations of CO2 adjacent to the outer tangential epidermal walls, which enhances the uptake of CO2, and this could be followed by a carbon-concentrating mechanism (CCM) in the cytoplasm and/or chloroplasts. The lines of evidence for such an epidermal CCM are discussed, including evidence for special 'transfer cells' in some but not all seagrass leaves in the tangential inner walls of the epidermal cells. It is concluded that seagrasses have a CCM but that the case for concentration of CO2 at the site of Rubisco carboxylation is not proven.

© The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com. CO2-concentrating mechanisms (CCMs), based either on active transport of inorganic carbon (biophysical CCMs) or on biochemistry involving supplementary carbon fixation into C4 acids (C4 and CAM), play a major role in global primary productivity. However, the ubiquitous CO2-fixing enzyme in autotrophs, Rubisco, evolved at a time when atmospheric CO2 levels were very much higher than today and O2 was very low and, as CO2 and O2 approached (by no means monotonically), today's levels, at some time subsequently many organisms evolved a CCM that increased the supply of CO2 and decreased Rubisco oxygenase activity. Given that CO2 levels and other environmental factors have altered considerably between when autotrophs evolved and the present day, and are predicted to continue to change into the future, we here examine the drivers for, and possible timing of, evolution of CCMs. CCMs probably evolved when CO2 fell to 2-16 times the present atmospheric level, depending on Rubisco kinetics. We also assess the effects of other key environmental factors such as temperature and nutrient levels on CCM activity and examine the evidence for evolutionary changes in CCM activity and related cellular processes as well as limitations on continuity of CCMs through environmental variations.

Contents 516 I. 516 II. 518 III. 518 IV. 521 V. 523 VI. 523 VII. 526 526 References 526 SUMMARY: The relevance of infochemicals in the relationships between organisms is emerging as a fundamental aspect of aquatic ecology. Exchanges of chemical cues are likely to occur not only between organisms of different species, but also between conspecific individuals. Especially intriguing is the investigation of chemical communication in microalgae, because of the relevance of these organisms for global primary production and their key role in trophic webs. Intraspecific communication between algae has been investigated mostly in relation to sexuality and mating. The literature also contains information on other types of intraspecific chemical communication that have not always been explicitly tagged as ways to communicate to conspecifics. However, the proposed role of certain compounds as intraspecific infochemicals appears questionable. In this article, we make use of this plethora of information to describe the various instances of intraspecific chemical communication between conspecific microalgae and to identify the common traits and ecological significance of intraspecific communication. We also discuss the evolutionary implications of intraspecific chemical communication and the mechanisms by which it can be inherited. A special focus is the genetic diversity among conspecific algae, including the possibility that genetic diversity is an absolute requirement for intraspecific chemical communication.

Acute low back pain (ALBP) causes rapid deterioration of paraspinal muscle function. The underlying neurophysiology is poorly understood. We therefore carried out this observational study in patients with ALBP to characterize motor unit (MU) activity in deep lumbar multifidus (LM) muscle and compare with our previous findings from pain-free subjects. Nine subjects (1 woman; age 26–59 yr) with ALBP duration of 1–21 days were recruited from outpatient clinics. Fine wire electromyography (EMG) electrodes were implanted bilaterally at the painful spinal level under computer tomography guidance. EMG was recorded during spontaneous sitting and standing, and during voluntary force production. Linear mixed models were utilized to test or control for the effects of a number of predefined variables. Compared with sitting, standing increased total duration of EMG activity, median MU discharge rate, interspike interval variability, and common drive measured as common drive coefficients (CDC) derived from concurrently active MU pairs. Median discharge rate in 73 MUs was 5.5 and 6.6 pulses per second (pps) during spontaneous sitting and standing, and 7.2 pps during voluntary force production. Interspike interval variability was lower during voluntary tasks than during spontaneous force production. Common drive was less pronounced in bilateral vs. unilateral unit pairs, also in spontaneous standing. This difference was not seen in our previous pain-free subjects, suggesting altered bilateral control of the spine in ALBP. The distribution of CDC values was not a homogeneous continuum but could be seen as two partially overlapping populations of CDC distributions. NEW & NOTEWORTHY We implanted fine-wire electrodes in the deepest part of axial postural muscles in patients with acute low back pain and characterized their motor unit activity. We found less pronounced common drive to the two sides of the spine compared with pain-free subjects, suggesting a different postural control strategy in patients with acute low back pain. An unexpected finding was that common drive coefficient values appeared to consist of two partially overlapping populations of normal distributions.

Gene and protein sequences, corresponding sequence alignment sand inferred phylogenies from the study "Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweedsNeoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds". #----------------------# # SEQUENCES # #----------------------# HOMCHL*.fltr.nt.fa nucleotidic sequences without need of scaffolding HOMCHL*.fltr.nt.no_scaffold.fa nucleotidic sequences not scaffolded HOMCHL*.fltr.nt.scaffold.fa nucleotidic sequences scaffolded HOMCHL*.fltr.aa.align.fa amino acid sequences without need of scaffolding HOMCHL*.fltr.aa.align.no_scaffold.fa amino acid sequences not scaffolded HOMCHL*.fltr.aa.align.scaffold.fa amino acid sequences scaffolded #----------------------# # ALIGNMENTS # #----------------------# HOMCHL*.fltr.nt.align.fa alignment of nucleotidic sequences without need of scaffolding HOMCHL*.fltr.nt.no_scaffold.align.fa alignment of nucleotidic sequences not scaffolded HOMCHL*.fltr.nt.scaffold.align.fa alignment of nucleotidic sequences scaffolded HOMCHL*.fltr.aa.align.align.fa alignment of amino acid sequences without need of scaffolding HOMCHL*.fltr.aa.align.no_scaffold.align.fa alignment of amino acid sequences not scaffolded HOMCHL*.fltr.aa.align.scaffold.align.fa alignment of amino acid sequences scaffolded HOMCHL*.fltr.nt.align.trim.fa trim alignment of nucleotidic sequences without need of scaffolding HOMCHL*.fltr.nt.no_scaffold.align.trim.fa trim alignment of nucleotidic sequences not scaffolded HOMCHL*.fltr.nt.scaffold.align.trim.fa trim alignment of nucleotidic sequences scaffolded HOMCHL*.fltr.aa.align.align.trim.fa trim alignment of amino acid sequences without need of scaffolded HOMCHL*.fltr.aa.align.no_scaffold.align.trim.fa trim alignment of amino acid sequences not scaffolded HOMCHL*.fltr.aa.align.scaffold.align.trim.fa trim alignment of amino acid sequences scaffolded #--------------------------------# # PHYLOGENETIC TREES # #--------------------------------# allgenes_coreGF_aa_noscaffold.C20.contree coreGF concatenated ML tree, no scaffold, C20 mixture model allgenes_coreGF_aa_noscaffold.contree coreGF concatenated ML tree, no scaffold, gene-wise partition allgenes_coreGF_aa_noscaffold.trim.C20.contree coreGF concatenated ML tree, no scaffold, trimmed alignment, C20 mixture model allgenes_coreGF_aa_noscaffold.trim.contree coreGF concatenated ML tree, no scaffold, trimmed alignment, gene-wise partition allgenes_coreGF_aa_scaffold.C20.contree coreGF concatenated ML tree, scaffold, C20 mixture model allgenes_coreGF_aa_scaffold.contree coreGF concatenated ML tree, scaffold, gene-wise partition allgenes_coreGF_aa_scaffold.trim.C20.contree coreGF concatenated ML tree, scaffold, trimmed alignment, C20 mixture model allgenes_coreGF_aa_scaffold.trim.contree coreGF concatenated ML tree, scaffold, trimmed alignment, gene-wise partition allgenes_UlvoGF_aa_noscaffold.C20.contree ulvoGF concatenated ML tree, no 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tree, no scaffold, trimmed alignment, gene-wise partition, Ignatius excluded allgenes_coreGF_aa_scaffold.noIgn.contree coreGF concatenated ML tree, scaffold, gene-wise partition, Ignatius excluded allgenes_coreGF_aa_scaffold.trim.contree coreGF concatenated ML tree, scaffold, trimmed alignment, gene-wise partition, Ignatius excluded allgenes_UlvoGF_aa_noscaffold.contree ulvoGF concatenated ML tree, no scaffold, gene-wise partition, Ignatius excluded allgenes_UlvoGF_aa_noscaffold.trim.contree ulvoGF concatenated ML tree, no scaffold, trimmed alignment, gene-wise partition, Ignatius excluded allgenes_UlvoGF_aa_scaffold.contree ulvoGF concatenated ML tree, scaffold, gene-wise partition, Ignatius excluded allgenes_UlvoGF_aa_scaffold.trim.contree ulvoGF concatenated ML tree, scaffold, trimmed alignment, gene-wise partition, Ignatius excluded ASTRAL_noscaffold_output.BS.tre coreGF coalescence-based tree, no scaffold, MLBS ASTRAL_noscaffold_output.tre coreGF coalescence-based tree, no scaffold, BestML ASTRAL_noscaffold_output.trim.BS.tre coreGF coalescence-based tree, no scaffold, trimmed alignment, MLBS ASTRAL_noscaffold_output.trim.tre coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML ASTRAL_scaffold_output.BS.tre coreGF coalescence-based tree, scaffold, MLBS ASTRAL_scaffold_output.tre coreGF coalescence-based tree, scaffold, BestML ASTRAL_scaffold_output.trim.BS.tre coreGF coalescence-based tree, scaffold, trimmed alignment, MLBS ASTRAL_scaffold_output.trim.tre coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML ASTRAL_UlvoGF_noscaffold_output.BS.tre ulvoGF coalescence-based tree, no scaffold, MLBS ASTRAL_UlvoGF_noscaffold_output.tre ulvoGF coalescence-based tree, no scaffold, BestML ASTRAL_UlvoGF_noscaffold_output.trim.BS.tre ulvoGF coalescence-based tree, no scaffold, trimmed alignment, MLBS ASTRAL_UlvoGF_noscaffold_output.trim.tre ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML ASTRAL_UlvoGF_scaffold_output.BS.tre ulvoGF coalescence-based tree, scaffold, MLBS ASTRAL_UlvoGF_scaffold_output.tre ulvoGF coalescence-based tree, scaffold, BestML ASTRAL_UlvoGF_scaffold_output.trim.BS.tre ulvoGF coalescence-based tree, scaffold, trimmed alignment, MLBS ASTRAL_UlvoGF_scaffold_output.trim.tre ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded ASTRAL_noscaffold_output.BS.noIgn.tre coreGF coalescence-based tree, no scaffold, MLBS, Ignatius excluded ASTRAL_noscaffold_output.noIgn.tre coreGF coalescence-based tree, no scaffold, BestML, Ignatius excluded ASTRAL_noscaffold_output.BS.trim.noIgn.tre coreGF coalescence-based tree, no scaffold, trimmed alignment, MLBS, Ignatius excluded ASTRAL_noscaffold_output.noIgn.tre coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded ASTRAL_scaffold_output.BS.noIgn.tre coreGF coalescence-based tree, scaffold, MLBS, Ignatius excluded ASTRAL_scaffold_output.BS.trim.noIgn.tre coreGF coalescence-based tree, scaffold, BestML, Ignatius excluded ASTRAL_scaffold_output.noIgn.tre coreGF coalescence-based tree, scaffold, trimmed alignment, MLBS , Ignatius excluded ASTRAL_scaffold_output.trim.noIgn.tre coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded ASTRAL_UlvoGF_noscaffold_output.BS.noIgn.tre ulvoGF coalescence-based tree, no scaffold, MLBS, Ignatius excluded ASTRAL_UlvoGF_noscaffold_output.noIgn.tre ulvoGF coalescence-based tree, no scaffold, BestML, Ignatius excluded ASTRAL_UlvoGF_noscaffold_output.trim.BS.noIgn.tre ulvoGF coalescence-based tree, no scaffold, trimmed alignment, MLBS, Ignatius excluded ASTRAL_UlvoGF_noscaffold_output.trim.noIgn.tre ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded ASTRAL_UlvoGF_scaffold_output.BS.noIgn.tre ulvoGF coalescence-based tree, scaffold, MLBS, Ignatius excluded ASTRAL_UlvoGF_scaffold_output.noIgn.tre ulvoGF coalescence-based tree, scaffold, BestML, Ignatius excluded ASTRAL_UlvoGF_scaffold_output.trim.BS.noIgn.tre ulvoGF coalescence-based tree, scaffold, trimmed alignment, MLBS, Ignatius excluded ASTRAL_UlvoGF_scaffold_output.trim.noIgn.tre ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded 02_*.chronogram time-calibrated trees, consult Table S6 for details 03_*.chronogram time-calibrated trees, consult Table S6 for details_*.chronogram time-calibrated tress, consult Table S6 for details #---------------------------------------------------------------------------------------------------------------------------------------# # for questions and additional info regarding the datasets, please contact andrea.delcortona@gmail.com # #----------------------------------------------------------------------------------------------------------------------------------------#

© 2019 John Wiley & Sons Ltd Aim: Most protist plankton are mixotrophic, with potential to engage in photoautotrophy and phagotrophy; however, the ecology of these organisms has been misdiagnosed for over a century. A large proportion of these organisms are constitutive mixotrophs (CMs), with an innate ability to photosynthesize. Here, for the first time, an analysis is presented of the biogeography of CMs across the oceans. Location: Global marine ecosystems. Time period: 1970–2018. Major taxa studied: Marine planktonic protists. Methods: Records for CM species, primarily from the Ocean Biogeographic Information System (OBIS), were grouped by taxonomy and size to evaluate sampling efforts across Longhurst's oceanic provinces. Biases were evaluated through nonparametric tests and multivariate analysis. Biogeographies of CMs from OBIS data were compared with data from studies that specifically targeted these organisms. Results: Constitutive mixotrophs of different taxonomic groups, across all size ranges, are ubiquitous. However, strong database biases were detected with respect to organism size, taxonomic groups and region. A strong bias was seen towards dinophytes. Species

Photosynthesis in the seagrass Zostera muelleri remains poorly understood. We investigated the effect of reduced irradiance on the incorporation of

The term Blue Carbon (BC) was first coined a decade ago to describe the disproportionately large contribution of coastal vegetated ecosystems to global carbon sequestration. The role of BC in climate change mitigation and adaptation has now reached international prominence. To help prioritise future research, we assembled leading experts in the field to agree upon the top-ten pending questions in BC science. Understanding how climate change affects carbon accumulation in mature BC ecosystems and during their restoration was a high priority. Controversial questions included the role of carbonate and macroalgae in BC cycling, and the degree to which greenhouse gases are released following disturbance of BC ecosystems. Scientists seek improved precision of the extent of BC ecosystems; techniques to determine BC provenance; understanding of the factors that influence sequestration in BC ecosystems, with the corresponding value of BC; and the management actions that are effective in enhancing this value. Overall this overview provides a comprehensive road map for the coming decades on future research in BC science., P.I.M. and C.E.L. were supported by an Australian Research Council Linkage Project (LP160100242). C.M.D. was supported by baseline funding from King Abdullah University of Science and Technology. T.K. and K.W. were supported by JSPS KAKENHI (18H04156) and the Environment Research and Technology Development Fund (S-14) of the Ministry of the Environment, Japan. B.D.E. was supported by Australian Research Council grants DP160100248 and LP150100519. D.A.S. was supported by the UK Natural Environment Research Council (NE/K008439/1), and D.K.J. was supported by the CARMA project (8021-00222B), funded by the Independent Research Fund Denmark. Funding was provided to P.M. by the Generalitat de Catalunya (MERS, 2017SGR 1588) and an Australian Research Council LIEF Project (LE170100219). This work is contributing to the ICTA ‘Unit of Excellence’ (MinECo, MDM2015-0552). O.S. was supported by an ARC DECRA (DE170101524). N.M. was supported by the Spanish Ministry of Economy, Industry and Competitiveness (MedShift project). N.B. was supported by the UK Research Councils under Natural Environment Research Council award NE/N013573/1. J.W.F. was supported by the US National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Grant No. DEB-1237517. R.S. had the support of FCT, project FCT UID/MAR/00350/2018. I.E.H. was supported by Ramon y Cajal Fellowship RYC2014-14970, co-funded by the Conselleria d’Innovació, Recerca i Turisme of the Balearic Government and the Spanish Ministry of Economy, Industry and Competitiveness. The University of Dundee is a registered Scottish charity, no. 015096. J.P.M. was supported by the Smithsonian Institution and the National Science Foundation Long-Term Research in Environmental Biology Program (DEB-0950080, DEB-1457100, DEB-1557009).

7 pages, 5 figures, supplementary material http://advances.sciencemag.org/cgi/content/full/5/8/eaaw8855/DC1, All known phototrophic metabolisms on Earth rely on one of three categories of energy-converting pigments: chlorophyll-a (rarely -d), bacteriochlorophyll-a (rarely -b), and retinal, which is the chromophore in rhodopsins. While the significance of chlorophylls in solar energy capture has been studied for decades, the contribution of retinal-based phototrophy to this process remains largely unexplored. We report the first vertical distributions of the three energy-converting pigments measured along a contrasting nutrient gradient through the Mediterranean Sea and the Atlantic Ocean. The highest rhodopsin concentrations were observed above the deep chlorophyll-a maxima, and their geographical distribution tended to be inversely related to that of chlorophyll-a. We further show that proton-pumping proteorhodopsins potentially absorb as much light energy as chlorophyll-a–based phototrophy and that this energy is sufficient to sustain bacterial basal metabolism. This suggests that proteorhodopsins are a major energy-transducing mechanism to harvest solar energy in the surface ocean, This project was founded by the Marie Curie Actions-International Outgoing Fellowships (project 253970), the U.S. National Science Foundation grant OCE1335269, the Simons Foundation award 509727, and the Gordon and Betty Moore Foundation Marine Microbiology Initiative award 3779. J.A. and J.M.G. were supported by the Spanish project HOTMIX (CTM2011-30010-C02-MAR). The University of Dundee is a registered Scottish charity, no. SC015096

Thylakoids are flattened sacs isolated from other membranes; cristae are attached to the rest of the inner mitochondrial membrane by the crista junction, but the crista lumen is separated from the intermembrane space. The shape of thylakoids and cristae involves membranes with small (5-30 nm) radii of curvature. While the mechanism of curvature is not entirely clear, it seems to be largely a function of Curt proteins in thylakoids and Mitochondrial Organising Site and Crista Organising Centre proteins and oligomeric FOF1 ATP synthase in cristae. A subordinate, or minimal, role is attributable to lipids with areas of their head group area greater (convex leaflet) or smaller (concave leaflet) than the area of the lipid tail; examples of the latter group are monogalactosyldiglyceride in thylakoids and cardiolipin in cristae. The volume per unit area on the lumen side of the membrane is less than that of the chloroplast stroma or cyanobacterial cytosol for thylakoids, and mitochondrial matrix for cristae. A low volume per unit area of thylakoids and cristae means a small lumen width that is the average of wider spaces between lipid parts of the membranes and the narrower gaps dominated by extra-membrane components of transmembrane proteins. These structural constraints have important implications for the movement of the electron carriers plastocyanin and cytochrome c6 (thylakoids) and cytochrome c (cristae) and hence the separation of the membrane-associated electron donors to, and electron acceptors from, these water-soluble electron carriers. The donor/acceptor pairs, are the cytochrome fb6Fenh complex and P700+ in thylakoids, and Complex III and Complex IV of cristae. The other energy flux parallel to the membranes is that of the proton motive force generated by redox-powered H+ pumps into the lumen to the proton motive force use in ATP synthesis by H+ flux from the lumen through the ATP synthase. For both the electron transport and proton motive force movement, concentration differences of reduced and oxidised electron carriers and protonated and deprotonated pH buffers are involved. The need for diffusion along a congested route of these energy transfer agents may limit the separation of sources and sinks parallel to the membranes of thylakoids and cristae.

Contrary to the current paradigm, competition experiments showed that green algae defeated cyanobacteria at low CO2 levels, whereas cyanobacteria with high-flux carbon uptake systems became stronger competitors at elevated CO2., Traditionally, it has often been hypothesized that cyanobacteria are superior competitors at low CO2 and high pH in comparison with eukaryotic algae, owing to their effective CO2-concentrating mechanism (CCM). However, recent work indicates that green algae can also have a sophisticated CCM tuned to low CO2 levels. Conversely, cyanobacteria with the high-flux bicarbonate uptake system BicA appear well adapted to high inorganic carbon concentrations. To investigate these ideas we studied competition between three species of green algae and a bicA strain of the harmful cyanobacterium Microcystis aeruginosa at low (100 ppm) and high (2000 ppm) CO2. Two of the green algae were competitively superior to the cyanobacterium at low CO2, whereas the cyanobacterium increased its competitive ability with respect to the green algae at high CO2. The experiments were supported by a resource competition model linking the population dynamics of the phytoplankton species with dynamic changes in carbon speciation, pH and light. Our results show (i) that competition between phytoplankton species at different CO2 levels can be predicted from species traits in monoculture, (ii) that green algae can be strong competitors under CO2-depleted conditions, and (iii) that bloom-forming cyanobacteria with high-flux bicarbonate uptake systems will benefit from elevated CO2 concentrations.

‘Multiple drivers’ (also termed ‘multiple stressors’) is the term used to describe the cumulative effects of multiple environmental factors on organisms or ecosystems. Here, we consider ocean acidification as a multiple driver because many inorganic carbon parameters are changing simultaneously, including total dissolved inorganic carbon, CO2, HCO3–, CO32–, H+ and CaCO3 saturation state. With the rapid expansion of ocean acidification research has come a greater understanding of the complexity and intricacies of how these simultaneous changes to the seawater carbonate system are affecting marine life. We start by clarifying key terms used by chemists and biologists to describe the changing seawater inorganic carbon system. Then, using key groups of non-calcifying (fish, seaweeds, diatoms) and calcifying (coralline algae, coccolithophores, corals, molluscs) organisms, we consider how various physiological processes are affected by different components of the carbonate system.