John A. Raven

James Hutton Institute, Aberdeen, Scotland, United Kingdom

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Publications (493)

  • Source
    Michel Lavoie · John A Raven · Maurice Levasseur
    [Show abstract] [Hide abstract] ABSTRACT: Little information is available on the energetics of buoyancy modulation in aflagellate phytoplankton, which comprise the majority of autotrophic cells found in the ocean. Here we computed for three aflagellate species of marine phytoplankton (Emiliania huxleyi, Thalassiosira pseudonana, and Ethmodiscus rex) the theoretical minimum energy cost as photons absorbed and nitrogen resource required of the key physiological mechanisms (i.e. replacement of quaternary ammonium by dimethylsulfoniopropionate, storage of polysaccharides, and cell wall biosynthesis) affecting the cell's vertical movement as a function of nitrogen (N) availability. These energy costs were also normalized to the capacity of each buoyancy mechanism to modulate sinking or rising rates based on Stokes’ law. The three physiological mechanisms could act as ballast in the three species tested in conditions of low N availability at a low fraction (<11.9%) of the total photon energy cost for growth. Cell wall formation in E. huxleyi was the least costly ballast strategy whereas in T. pseudonana the photon energy cost of the three ballast strategies were similar. In E. rex, carbohydrate storage and mobilization appear to be energetically cheaper than modulations in organic solute synthesis to achieve vertical migration. This supports the carbohydrate ballast strategy for vertical migration for this species, but argues against the theory of replacement of low or high density organic solutes. The present study brings new insights into the energy cost and potential selective advantage of several strategies modulating the buoyancy of aflagellate marine phytoplankton. This article is protected by copyright. All rights reserved.
    Full-text Article · Apr 2016 · Journal of Phycology
  • John A Raven · Timothy D Colmer
    [Show abstract] [Hide abstract] ABSTRACT: Mosses are among the earliest branching embryophytes and probably originated not later than the early Ordovician when atmospheric CO2 was higher and O2 was lower than today. The C3 biochemistry and physiology of their photosynthesis suggests, by analogy with tracheophytes, that growth of extant bryophytes in high CO2 approximating Ordovician values would increase the growth rate. This occurs for many mosses, including Physcomitrella patens in suspension culture, although recently published transcriptomic data on this species at high CO2 and present-day CO2 show down-regulation of the transcription of several genes related to photosynthesis. It would be useful if transcriptomic (and proteomic) data comparing growth conditions are linked to measurements of growth and physiology on the same, or parallel, cultures. Mosses (like later-originating embryophytes) have been subject to changes in bulk atmospheric CO2 and O2 throughout their existence, with evidence, albeit limited, for positive selection of moss Rubisco. Extant mosses are subject to a large range of CO2 and O2 concentrations in their immediate environments, especially aquatic mosses, and mosses are particularly influenced by CO2 generated by, and O2 consumed by, soil chemoorganotrophy from organic C produced by tracheophytes (if present) and bryophytes.
    Article · Feb 2016 · Journal of Experimental Botany
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    [Show abstract] [Hide abstract] ABSTRACT: Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic “phytoplankton” and phagotrophic “microzooplankton”. However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an eco-physiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their structures.
    Full-text Article · Feb 2016 · Protist
  • John A. Raven · Mario Giordano
    [Show abstract] [Hide abstract] ABSTRACT: Algae can use a wide range of combined N sources. All of them can use NH4+, and probably also use urea and one of more amino acids; most of them can also use NO2− and NO3−, and some can use betaines and/or purines. Transport of combined N into cells very often uses H+ or Na+ symport. Two cations transported per anionic N species, and one cation transported per neutral N species, enables the electrical potential difference across the membrane generated by active cation efflux to be used to increase the accumulation ratio inside:outside of the combined N species. Cationic N forms, e.g. NH4+, sometimes occur at very low concentrations in the natural environment, and cation symport can increase the steady-state NH4+ concentration. The transporters have been to some extent characterised at the molecular level, especially for the plasmalemma. Assimilation of inorganic N species into organic N within the cell use well-established pathways, i.e. NO3− reductase, NO2− reductase, and glutamine synthetase – glutamine-oxoglutarate aminotransferase enzymes. N assimilation, and especially the initial step (NO3− reductase), are under more direct redox control in microalgae than in vascular plants. Combined N species which as NO and NO3− are involved in signalling within the cell, but extent to which they modulate metabolism in response to internal and external cues needs clarification. It is important to bear in mind that the conclusions drawn here generally come from work on relatively few microalgal species, and generalisations should be viewed with caution.
    Chapter · Jan 2016
  • Article · Jan 2016 · Metallomics
  • John A Raven · John Beardall
    [Show abstract] [Hide abstract] ABSTRACT: It is difficult to distinguish influx and efflux of inorganic C in photosynthesizing tissues; this article examines what is known and where there are gaps in knowledge. Irreversible decarboxylases produce CO2, and CO2 is the substrate/product of enzymes that act as carboxylases and decarboxylases. Some irreversible carboxylases use CO2; others use HCO3 –. The relative role of permeation through the lipid bilayer versus movement through CO2-selective membrane proteins in the downhill, non-energized, movement of CO2 is not clear. Passive permeation explains most CO2 entry, including terrestrial and aquatic organisms with C3 physiology and biochemistry, terrestrial C4 plants and all crassulacean acid metabolism (CAM) plants, as well as being part of some mechanisms of HCO3 – use in CO2 concentrating mechanism (CCM) function, although further work is needed to test the mechanism in some cases. However, there is some evidence of active CO2 influx at the plasmalemma of algae. HCO3 – active influx at the plasmalemma underlies all cyanobacterial and some algal CCMs. HCO3 – can also enter some algal chloroplasts, probably as part of a CCM. The high intracellular CO2 and HCO3 – pools consequent upon CCMs result in leakage involving CO2, and occasionally HCO3 –. Leakage from cyanobacterial and microalgal CCMs involves up to half, but sometimes more, of the gross inorganic C entering in the CCM; leakage from terrestrial C4 plants is lower in most environments. Little is known of leakage from other organisms with CCMs, though given the leakage better-examined organisms, leakage occurs and increases the energetic cost of net carbon assimilation.
    Article · Oct 2015 · Journal of Experimental Botany
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    [Show abstract] [Hide abstract] ABSTRACT: Anthropogenic activities are altering total nutrient loads to many estuaries and freshwaters, resulting in high loads not only of total nitrogen (N), but in some cases, of chemically reduced forms, notably . Long thought to be the preferred form of N for phytoplankton uptake, may actually suppress overall growth when concentrations are sufficiently high. has been well known to be inhibitory or repressive for uptake and assimilation, but the concentrations of that promote vs. repress uptake, assimilation, and growth in different phytoplankton groups and under different growth conditions are not well understood. Here, we review N metabolism first in a “generic” eukaryotic cell, and the contrasting metabolic pathways and regulation of and when these substrates are provided individually under equivalent growth conditions. Then the metabolic interactions of these substrates are described when both are provided together, emphasizing the cellular challenge of balancing nutrient acquisition with photosynthetic energy balance in dynamic environments. Conditions under which dissipatory pathways such as dissimilatory / reduction to and photorespiration that may lead to growth suppression are highlighted. While more is known about diatoms, taxon-specific differences in and metabolism that may contribute to changes in phytoplankton community composition when the composition of the N pool changes are presented. These relationships have important implications for harmful algal blooms, development of nutrient criteria for management, and modeling of nutrient uptake by phytoplankton, particularly in conditions where eutrophication is increasing and the redox state of N loads is changing.
    Full-text Article · Oct 2015
  • Dianne Edwards · Lesley Cherns · John A. Raven
    [Show abstract] [Hide abstract] ABSTRACT: The Ordovician and Silurian periods were times of major geological activity as regards palaeogeography, volcanism and climate change, the last of these evidenced by a series of cooling episodes and glaciations that climaxed in the Hirnantian (Late Ordovician). The presence of cryptospores in the Darriwilian (Middle Ordovician) marked the advent of higher plants on land. A critical survey of direct (mega- and microfossils) and some indirect evidence in succeeding rocks indicates the presence of algae, Bacteria, Cyanobacteria, Fungi, probable lichens, cryptophytes and basal tracheophytes. Similar associations of photosynthesizers and decomposers occur today in cryptogamic covers (CCs), for example biological crusts, except that bryophytes replace cryptophytes (basal embryophytes) and tracheophytes are absent. Thus, extant CCs, which make significant contributions today to global carbon and nitrogen fixation and prevention of erosion, provide an excellent analogue for the impacts of early land vegetation on both lithosphere and atmosphere. As a prerequisite to assessing impacts in Ordovician–Silurian times, with particular consideration of parameters used by climate modellers, the effects of a number of abiotic factors on the growth and survival of extant cryptogamic ground covers and their environmental impacts are reviewed. Factors include photosynthetically active radiation, ultraviolet radiation, temperature, water, oxygen, carbon dioxide, nitrogen, phosphorus, iron, surface roughness and albedo. A survey of the nature and extent of weathering facilitated by such vegetation concludes that it was limited based on depth of weathering when compared with that from rooted tracheophytes today, with minor effects on carbon dioxide drawdown. As global net productivity from Ordovician–Silurian CCs was very probably lower than today, and while the small fraction of intractable material in their organic carbon would have resulted in a more rapid turnover of terrestrial biomass, we conclude that there was decreased possibility of long-term organic carbon burial. Hence, there would have been very limited increase in atmospheric oxygen and decrease in carbon dioxide resulting from carbon burial.
    Article · Aug 2015 · Palaeontology
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    [Show abstract] [Hide abstract] ABSTRACT: This study presents the first in-depth analysis of CO2 limitation on the biomass productivity of the biofuel candidate marine microalga Nannochloropsis oculata. Net photosynthesis decreased by 60 % from 125 to 50 μmol O 2 L(-1) h(-1) over a 12 h light cycle as a direct result of carbon limitation. Continuous dissolved O2 and pH measurements were used to develop a detailed diurnal mechanism for the interaction between photosynthesis, gas exchange and carbonate chemistry in the photo-bioreactor. Gas exchange determined the degree of carbon limitation experienced by the algae. Carbon limitation was confirmed by delivering more CO2 , which increased net photosynthesis back to its steady-state maximum. This study highlights the importance of maintaining replete carbon concentrations in photo-bioreactors and other culturing facilities, either by constant pH operation or preferably by designing a feedback loop based on the dissolved O2 concentration. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Full-text Article · Jul 2015 · ChemSusChem
  • John A Raven
    [Show abstract] [Hide abstract] ABSTRACT: Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email:
    Article · Jun 2015 · Journal of Experimental Botany
  • Keith Mott · John A Raven
    [Show abstract] [Hide abstract] ABSTRACT: It was with a deep sense of loss and immense sadness that those at Plant, Cell and Environment learnt of the death, on 9 February 2015, of Harry Smith FRS. Harry was one of the four founding editors of the journal, and its first Chief Editor. This article is protected by copyright. All rights reserved.
    Article · May 2015 · Plant Cell and Environment
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    Kevin J. Flynn · Michael St John · John A. Raven · [...] · Eileen E. Hofmann
    [Show abstract] [Hide abstract] ABSTRACT: We propose definitions in terminology to enhance ongoing collaborations between biologists and modellers on plankton ecology. Organism "functional type" should refer to commonality in ecology not biogeochemistry; the latter is largely an emergent property of the former, while alignment with ecology is also consistent with usage in terrestrial science. Adaptation should be confined, as in genetics, to consideration of species inter-generational change; most so-called "adaptive" plankton models are thus acclimative, modifying vital rates in response to stimuli. Trait trade-off approaches should ideally only be considered for describing intra-generational interactions; in applications between generations, and certainly between unrelated species, such concepts should be avoided. We suggest that systems biology approaches, through to complex adaptive/acclimative systems modelling, with explicit modelling of feedback processes (which we suggest should define "mechanistic" models), would provide realistic and flexible bases upon which to develop descriptions of functional type models. © 2015 The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: [email protected] /* */
    Full-text Article · May 2015 · Journal of Plankton Research
  • Mario Giordano · Matteo Palmucci · John A Raven
    [Show abstract] [Hide abstract] ABSTRACT: The Growth Rate Hypothesis (GRH) predicts a positive correlation between growth rate and RNA content, because growth depends on the protein synthesis machinery. The application of this hypothesis to photoautotrophic organisms has been questioned. We tested the GRH on one prasinophycean, Tetraselmis suecica and one chlorophycean Dunaliella salina, grown at three sulfate concentrations. Sulfate was chosen because its concentration in the oceans increased through geological time and apparently had a role in the evolutionary trajectories of phytoplankton. Cell protein content and P quota were positively related to the RNA content (r = 0.62 and r = 0.74, respectively). The correlation of the RNA content with growth rates (r = 0.95) indicates that the GRH was valid for these species, when growth rates were below 0.82 d(-1) . This article is protected by copyright. All rights reserved.
    Article · Apr 2015 · Plant Cell and Environment
  • John A. Raven
    Article · Apr 2015 · Journal of Phycology
  • John A Raven · Howard Griffiths
    [Show abstract] [Hide abstract] ABSTRACT: The role of photosynthesis by reproductive structures during grain-filling has important implications for cereal breeding, but the methods for assessing the contribution by reproductive structures to grain-filling are invasive and prone to compensatory changes elsewhere in the plant. A technique analysing the natural abundance of stable carbon isotopes in soluble carbohydrates has significant promise. However, it depends crucially on there being no more than two sources of organic carbon (leaf and ear/awn), with significantly different (13)C:(12)C ratios and no secondary fractionation during grain-filling. The role of additional peduncle carbohydrate reserves represents a potential means for N remobilization, as well as for hydraulic continuity during grain-filling. The natural abundance of the stable isotopes of carbon and oxygen are also useful for exploring the influence of reproduction on whole plant carbon and water relations and have been used to examine the resource costs of reproduction in females and males of dioecious plants. Photosynthesis in reproductive structures is widespread among oxygenic photosynthetic organisms, including many clades of algae and embryophytes of different levels of complexity. The possible evolutionary benefits of photosynthesis in reproductive structures include decreasing the carbon cost of reproduction and 'use' of transpiratory loss of water to deliver phloem-immobile calcium Ca(2+) and silicon [Si(OH)4] via the xylem. The possible costs of photosynthesis in reproductive structures are increasing damage to DNA from photosynthetically active, and hence UV-B, radiation and the production of reactive oxygen species. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email:
    Article · Feb 2015 · Journal of Experimental Botany
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    [Show abstract] [Hide abstract] ABSTRACT: Earth will become uninhabitable within 2-3 Gyr as a result of the moving boundaries of the habitable zone caused by the increasing luminosity of the Sun. Predictions about the future of habitable conditions on Earth include a decline in species diversity and habitat extent, ocean loss and changes in the magnitudes of geochemical cycles. However, testing these predictions on the present-day Earth is difficult. The discovery of a planet that is a near analogue to the far future Earth could provide a means to test these predictions. Such a planet would need to have an Earth-like biosphere history, requiring it to have been in its system's habitable zone (HZ) for Gyr-long periods during the system's past, and to be approaching the inner-edge of the HZ at present. Here we assess the possibility of finding this very specific type of exoplanet and discuss the benefits of analysing older Earths in terms of improving our understanding of long-term geological and bio-geological processes. As an illustrative example, G stars within 10 parsecs are assessed as potential old-Earth-analogue hosts. Surface temperature estimates for hypothetical inner-HZ Earth analogues are used to determine whether any such planets in these systems would be at the right stage in their late-habitable lifetimes to exhibit detectable biosignatures. Predictions from planet formation studies and biosphere evolution models suggest that only 0.36% of G stars in the solar neighbourhood could host an old-Earth-analogue. However, if the development of an Earth-like biosphere is assumed to be rare, requiring a sequence of low-probability events to occur, then such planets are unlikely to be found in the solar neighbourhood - although 1000s could be present in the galaxy as a whole.
    Full-text Article · Feb 2015 · Astrobiology
  • Dale Radford · Milán Szabó · John A. Raven · Peter J. Ralph
    Article · Jan 2015 · European Journal of Phycology
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    Full-text Dataset · Nov 2014
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    Dataset: AP-AME
    Full-text Dataset · Nov 2014
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    Full-text Dataset · Nov 2014

Publication Stats

24k Citations


  • 2011
    • James Hutton Institute
      Aberdeen, Scotland, United Kingdom
  • 1974-2006
    • University of Adelaide
      • School of Earth and Environmental Sciences
      Tarndarnya, South Australia, Australia
  • 1975-2005
    • University of Dundee
      • • Division of Plant Science
      • • Division of Mathematics
      Dundee, Scotland, United Kingdom
  • 1993
    • Humboldt-Universität zu Berlin
      Berlín, Berlin, Germany