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This article is a collection of personal reflections and tributes from scientists who worked with Richard W. Eppley, a renowned scientist in the field of biological oceanography. Eppley's research focused on phytoplankton and their role in biogeochemical processes. The article highlights his contributions to the field and his impact on his students and colleagues. Eppley's career spanned many scientific cruises and he was known for his integrity and curiosity about the ocean. The article also provides a biography of Eppley, describing his personal life and interests outside of his scientific work. [Extracted from the article]

Phytoplankton in the ocean account for less than 1% of the global photosynthetic biomass, but contribute about 45% of the photosynthetically fixed carbon on Earth. This amazing production/biomass ratio implies a very high photosynthetic efficiency. But, how efficiently is the absorbed light used in marine photosynthesis? The introduction of picosecond and then femtosecond lasers for kinetic measurements in mid 1970s to 90 s was a revolution in basic photosynthesis research that vastly improved our understanding of the energy conversion processes in photosynthetic reactions. Until recently, the use of this technology in the ocean was not feasible due to the complexity of related instrumentation and the lack of picosecond lasers suitable for routine operation in the field. However, recent advances in solid-state laser technology and the development of compact data acquisition electronics led to the application of picosecond fluorescence lifetime analyses in the field. Here, we review the development of operational ultrasensitive picosecond fluorescence instruments to infer photosynthetic energy conversion processes in ocean ecosystems. This analysis revealed that, in spite of the high production/biomass ratio in marine phytoplankton, the photosynthetic energy conversion efficiency is exceptionally low—on average, ca. 50% of its maximum potential, suggesting that most of the contemporary open ocean surface waters are extremely nutrient deficient. [ABSTRACT FROM AUTHOR]

The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation–reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox (https://protein-redox-potential.web.app), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation–reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user‐contributed submissions with the intention of making it a valuable resource for researchers in this field. [ABSTRACT FROM AUTHOR]

Of the six elements incorporated into the major polymers of life, phosphorus is the least abundant on a global scale [E. Anders, M. Ebihara, Geochim. Cosmochim. Acta 46, 2363–2380 (1982)] and has been described as the “ultimate limiting nutrient” [T. Tyrrell, Nature 400, 525–531 (1999)]. In the modern ocean, the supply of dissolved phosphorus is predominantly sustained by the oxidative remineralization/recycling of organic phosphorus in seawater. However, in the Archean Eon (4 to 2.5 Ga), surface waters were anoxic and reducing. Here, we conducted photochemical experiments to test whether photodegradation of ubiquitous dissolved organic phosphorus could facilitate phosphorus recycling under the simulated Archean conditions. Our results strongly suggest that organic phosphorus compounds, which were produced by marine biota (e.g., adenosine monophosphate and phosphatidylserine) or delivered by meteorites (e.g., methyl phosphonate) can undergo rapid photodegradation and release inorganic phosphate into solution under anoxic conditions. Our experimental results and theoretical calculations indicate that photodegradation of organic phosphorus could have been a significant source of bioavailable phosphorus in the early ocean and would have fueled primary production during the Archean eon. [ABSTRACT FROM AUTHOR]

Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfide minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infinite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are finite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a finite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere. [ABSTRACT FROM AUTHOR]

Unicellular photoautotrophs adapt to variations in light intensity by changing the abundance of light harvest pigment-protein complexes (LHCs) on time scales of hours to days. This process requires a feedback signal between the plastid (where light intensity is sensed) to the nucleus (where the genes for LHCs are encoded). The signals must include heretofore unidentified transcription factors that modify the expression level of the LHCs. Analysis of the nuclear genome of the model diatom Phaeodactylum tricornutum revealed that all the lhc genes have potential binding sites for transcription factors belonging to the MYB-family proteins. Functional studies involving antisense RNA interference of a hypothetical protein with a MYB DNA-binding domain were performed. The resultant strains with altered photosynthetic and physiological characteristics lost their ability to acclimate to changes in irradiance; i.e., cellular chlorophyll content became independent of growth irradiance. Our results strongly suggest that the inter-organellar signaling cascade was disrupted, and the cell could no longer communicate the environmental signal from the plastid to the nucleus. Here, we identify, for the first time, an LHC Regulating Myb (LRM) transcription factor, which we propose is involved in lhc gene regulation and photoacclimation mechanisms in response to changes in light intensity. [ABSTRACT FROM AUTHOR]

The redox state of the plastoquinone (PQ) pool is a known sensor for retrograde signaling. In this paper, we asked, "does the redox state of the PQ pool modulate the saturation state of thylakoid lipids?" Data from fatty acid composition and mRNA transcript abundance analyses suggest a strong connection between these two aspects in a model marine diatom. Fatty acid profiles of Phaeodactylum tricornutum exhibited specific changes when the redox state of the PQ pool was modulated by light and two chemical inhibitors [3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) or 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB)]. Data from liquid chromatography with tandem mass spectrometry (LC–MS/MS) indicated a ca. 7–20% decrease in the saturation state of all four conserved thylakoid lipids in response to an oxidized PQ pool. The redox signals generated from an oxidized PQ pool in plastids also increased the mRNA transcript abundance of nuclear-encoded C16 fatty acid desaturases (FADs), with peak upregulation on a timescale of 6 to 12 h. The connection between the redox state of the PQ pool and thylakoid lipid saturation suggests a heretofore unrecognized retrograde signaling pathway that couples photosynthetic electron transport and the physical state of thylakoid membrane lipids. [ABSTRACT FROM AUTHOR]

In a rapidly warming world, we ask, "What limits the potential of marine diatoms to acclimate to elevated temperatures?," a group of ecologically successful unicellular eukaryotic photoautotrophs that evolved in a cooler ocean and are critical to marine food webs. To this end, we examined thermal tolerance mechanisms related to photosynthesis in the sequenced and transformable model diatom Phaeodactylum tricornutum. Data from transmission electron microscopy (TEM) and fatty acid methyl ester‐gas chromatography mass spectrometry (FAME‐GCMS) suggest that saturating thylakoid‐associated fatty acids allowed rapid (on the order of hours) thermal tolerance up to 28.5°C. Beyond this critical temperature, thylakoid ultrastructure became severely perturbed. Biophysical analyses revealed that electrochemical leakage through the thylakoid membranes was extremely sensitive to elevated temperature (Q10 of 3.5). Data suggest that the loss of the proton motive force (pmf) occurred even when heat‐labile photosystem II (PSII) was functioning, and saturation of thylakoid‐associated fatty acids was active. Indeed, growth was inhibited when leakage of pmf through thylakoid membranes was insufficiently compensated by proton input from PSII. Our findings provide a mechanistic understanding of the importance of rapid saturation of thylakoid‐associated fatty acids for ultrastructure maintenance and a generation of pmf at elevated temperatures. To the extent these experimental results apply, the ability of diatoms to generate a pmf may be a sensitive parameter for thermal sensitivity diagnosis in phytoplankton. [ABSTRACT FROM AUTHOR]

Variable fluorescence techniques are increasingly used to assess phytoplankton photosynthesis. All fluorescence techniques and models for photosynthetic electron transport rates (ETRs) are amplitude‐based and are subject to errors, especially when phytoplankton growth is nutrient‐limited. Here we develop a new, kinetic‐based approach to measure, directly and in absolute units, ETRs and to estimate growth rates in phytoplankton. We applied this approach to investigate the effects of nitrogen limitation on phytoplankton photophysiology and growth rates. Nutrient stress leads to a decrease in the quantum yield of photochemistry in Photosystem II (Fv/Fm); however, the relationship between Fv/Fm and growth rates is highly nonlinear, which makes it impossible to quantify the reduction in phytoplankton growth rates from Fv/Fm alone. In contrast, the decline in growth rates under nitrogen stress was proportional to the decrease in kinetic‐based photosynthetic rates. Our analysis suggests the kinetic fluorescence measurements markedly improve the accuracy of ETR measurements, as compared to classical amplitude‐based measurements. Fluorescence‐based methods for primary production rely on measurements of ETRs and then conversion to carbon fixation rates by using the electron yields of carbon fixation. The electron yields exhibit 10‐fold variability in natural phytoplankton communities and are strongly affected by nutrient limitation. Our results reveal that a decrease in the growth rates and the electron yields of carbon fixation is driven by, and can be quantified from, a decrease in photosynthetic turnover rates. We propose an algorithm to deduce the electron yields of carbon fixation, which greatly improve fluorescence‐based measurements of primary production and growth rates. [ABSTRACT FROM AUTHOR]

The West Antarctic Peninsula (WAP) is a highly productive polar ecosystem where phytoplankton dynamics are regulated by intense bottom‐up control from light and iron availability. Rapid climate change along the WAP is driving shifts in the mixed layer depth and iron availability. Elucidating the relative role of each of these controls and their interactions is crucial for understanding of how primary productivity will change in coming decades. Using a combination of ultra‐high‐resolution variable chlorophyll fluorescence together with fluorescence lifetime analyses on the 2017 Palmer Long Term Ecological Research cruise, we mapped the temporal and spatial variability in phytoplankton photophysiology across the WAP. Highest photosynthetic energy conversion efficiencies and lowest fluorescence quantum yields were observed in iron replete coastal regions. Photosynthetic energy conversion efficiencies decreased by ~ 60% with a proportional increase in quantum yields of thermal dissipation and fluorescence on the outer continental shelf and slope. The combined analysis of variable fluorescence and lifetimes revealed that, in addition to the decrease in the fraction of inactive reaction centers, up to 20% of light harvesting chlorophyll‐protein antenna complexes were energetically uncoupled from photosystem II reaction centers in iron‐limited phytoplankton. These biophysical signatures strongly suggest severe iron limitation of photosynthesis in the surface waters along the continental slope of the WAP. [ABSTRACT FROM AUTHOR]

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant enzyme on Earth. However, its catalytic rate per molecule of protein is extremely slow and the binding of the primary substrate, CO2, is competitively displaced by O2. Hence, carbon fixation by RuBisCO is highly inefficient; indeed, in higher C3 plants, about 30% of the time the enzyme mistakes CO2 for O2. Using genomic and structural analysis, we identify regions around the catalytic site that play key roles in discriminating between CO2 and O2. Our analysis identified positively charged cavities directly around the active site, which are expanded as the enzyme evolved with higher substrate specificity. The residues that extend these cavities have recently been under selective pressure, indicating that larger charged pockets are a feature of modern RuBisCOs, enabling greater specificity for CO2. This paper identifies a key structural feature that enabled the enzyme to evolve improved CO2 sequestration in an oxygen-rich atmosphere and may guide the engineering of more efficient RuBisCOs. [ABSTRACT FROM AUTHOR]

The oxidation states of manganese minerals in the geological record have been interpreted as proxies for the evolution of molecular oxygen in the Archean eon. Here we report that an Archean manganese mineral, rhodochrosite (MnCO3), can be photochemically oxidized by light under anoxic, abiotic conditions. Rhodochrosite has a calculated bandgap of about 5.4 eV, corresponding to light energy centering around 230 nm. Light at that wavelength would have been present on Earth's surface in the Archean, prior to the formation of stratospheric ozone. We show experimentally that the photooxidation of rhodochrosite in suspension with light centered at 230 nm produced H2 gas and manganite (?-MnOOH) with an apparent quantum yield of 1.37 × 10-3 moles hydrogen per moles incident photons. Our results suggest that manganese oxides could have formed abiotically on the surface in shallow waters and on continents during the Archean eon in the absence of molecular oxygen. [ABSTRACT FROM AUTHOR]

Life on Earth is driven by electron transfer reactions catalyzed by a suite of enzymes that comprise the superfamily of oxidoreductases (Enzyme Classification EC1). Most modern oxidoreductases are complex in their structure and chemistry and must have evolved from a small set of ancient folds. Ancient oxidoreductases from the Archean Eon between ca. 3.5 and 2.5 billion years ago have been long extinct, making it challenging to retrace evolution by sequence-based phylogeny or ancestral sequence reconstruction. However, three-dimensional topologies of proteins change more slowly than sequences. Using comparative structure and sequence profile-profile alignments, we quantify the similarity between proximal cofactor-binding folds and show that they are derived from a common ancestor. We discovered that two recurring folds were central to the origin of metabolism: ferredoxin and Rossmann-like folds. In turn, these two folds likely shared a common ancestor that, through duplication, recruitment, and diversification, evolved to facilitate electron transfer and catalysis at a very early stage in the origin of metabolism. [ABSTRACT FROM AUTHOR]

Hard, or stony, corals make rocks that can, on geological time scales, lead to the formation of massive reefs in shallow tropical and subtropical seas. In both historical and contemporary oceans, reef‐building corals retain information about the marine environment in their skeletons, which is an organic–inorganic composite material. The elemental and isotopic composition of their skeletons is frequently used to reconstruct the environmental history of Earth's oceans over time, including temperature, pH, and salinity. Interpretation of this information requires knowledge of how the organisms formed their skeletons. The basic mechanism of formation of calcium carbonate skeleton in stony corals has been studied for decades. While some researchers consider coral skeletons as mainly passive recorders of ocean conditions, it has become increasingly clear that biological processes play key roles in the biomineralization mechanism. Understanding the role of the animal in living stony coral biomineralization and how it evolved has profound implications for interpreting environmental signatures in fossil corals to understand past ocean conditions. Here we review historical hypotheses and discuss the present understanding of how corals evolved and how their skeletons changed over geological time. We specifically explain how biological processes, particularly those occurring at the subcellular level, critically control the formation of calcium carbonate structures. We examine the different models that address the current debate including the tissue–skeleton interface, skeletal organic matrix, and biomineralization pathways. Finally, we consider how understanding the biological control of coral biomineralization is critical to informing future models of coral vulnerability to inevitable global change, particularly increasing ocean acidification. [ABSTRACT FROM AUTHOR]

A descendant of the red algal lineage, diatoms are unicellular eukaryotic algae characterized by thylakoid membranes that lack the spatial differentiation of stroma and grana stacks found in green algae and higher plants. While the photophysiology of diatoms has been studied extensively, very little is known about the spatial organization of the multimeric photosynthetic protein complexes within their thylakoid membranes. Here, using cryoelectron tomography, proteomics, and biophysical analyses, we elucidate the macromolecular composition, architecture, and spatial distribution of photosystem II complexes in diatom thylakoid membranes. Structural analyses reveal 2 distinct photosystem II populations: loose clusters of complexes associated with antenna proteins and compact 2D crystalline arrays of dimeric cores. Biophysical measurements reveal only 1 photosystem II functional absorption cross section, suggesting that only the former population is photosynthetically active. The tomographic data indicate that the arrays of photosystem II cores are physically separated from those associated with antenna proteins. We hypothesize that the islands of photosystem cores are repair stations, where photodamaged proteins can be replaced. Our results strongly imply convergent evolution between the red and the green photosynthetic lineages toward spatial segregation of dynamic, functional microdomains of photosystem II supercomplexes. [ABSTRACT FROM AUTHOR]

A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no functional symmetric molecule has been constructed. It is hypothesized that extant proteins have drifted from their symmetric roots via gene duplication followed by mutations. Phylogenetic analyses of extant ferredoxins support the independent evolution of N- and C-terminal sequences, thereby allowing consensus-based design of symmetric 4Fe-4S molecules. All designs bind two [4Fe-4S] clusters and exhibit strongly reducing midpoint potentials ranging from -405 to -515 mV. One of these constructs efficiently shuttles electrons through a designed metabolic pathway in Escherichia coli. These finding establish that ferredoxins consisting of a symmetric core can be used as a platform to design novel electron transfer carriers for in vivo applications. Outer-shell asymmetry increases sequence space without compromising electron transfer functionality. [ABSTRACT FROM AUTHOR]

Summary: The reduction of elemental sulfur is an important energy‐conserving pathway in prokaryotes inhabiting geothermal environments, where sulfur respiration contributes to sulfur biogeochemical cycling. Despite this, the pathways through which elemental sulfur is reduced to hydrogen sulfide remain unclear in most microorganisms. We integrated growth experiments using Thermovibrio ammonificans, a deep‐sea vent thermophile that conserves energy from the oxidation of hydrogen and reduction of both nitrate and elemental sulfur, with comparative transcriptomic and proteomic approaches, coupled with scanning electron microscopy. Our results revealed that two members of the FAD‐dependent pyridine nucleotide disulfide reductase family, similar to sulfide‐quinone reductase and to NADH‐dependent sulfur reductase (NSR), respectively, are over‐expressed during sulfur respiration. Scanning electron micrographs and sulfur sequestration experiments indicated that direct access of T. ammonificans to sulfur particles strongly promoted growth. The sulfur metabolism of T. ammonificans appears to require abiotic transition from bulk elemental sulfur to polysulfide to nanoparticulate sulfur at an acidic pH, coupled to biological hydrogen oxidation. A coupled biotic‐abiotic mechanism for sulfur respiration is put forward, mediated by an NSR‐like protein as the terminal reductase. [ABSTRACT FROM AUTHOR]

Abstract: The geosphere and biosphere coevolved and influenced Earth's biological and mineralogical diversity. Changing redox conditions influenced the availability of different transition metals, which are essential components in the active sites of oxidoreductases, proteins that catalyze electron transfer reactions across the tree of life. Despite its relatively low abundance in the environment, cobalt (Co) is a unique metal in biology due to its importance to a wide range of organisms as the metal center of vitamin B12 (aka cobalamin, Cbl). Cbl is vital to multiple methyltransferase enzymes involved in energetically favorable metabolic pathways. It is unclear how Co availability is linked to mineral evolution and weathering processes. Here we examine important biological functions of Co, as well as chemical and geological factors that may have influenced the utilization of Co early in the evolution of life. Only 66 natural minerals are known to contain Co as an essential element. However, Co is incorporated as a minor element in abundant rock‐forming minerals, potentially representing a reliable source of Co as a trace element in marine systems due to weathering processes. We developed a mineral weathering model that indicates that dissolved Co was potentially more bioavailable in the Archean ocean under low S conditions than it is today. Mineral weathering, redox chemistry, Co complexation with nitrogen‐containing organics, and hydrothermal environments were crucial in the incorporation of Co in primitive metabolic pathways. These chemical and geological characteristics of Co can inform the biological utilization of other trace metals in early forms of life. [ABSTRACT FROM AUTHOR]

Oxidoreductases catalyze electron transfer reactions that ultimately provide the energy for life. A limited set of ancestral protein-metal modules are presumably the building blocks that evolved into this diverse protein family. However, the identity of these modules and their path to modern oxidoreductases is unknown. Using a comparative structural analysis approach, we identify a set of fundamental electron transfer modules that have evolved to form the extant oxidoreductases. Using transition metal-containing cofactors as fiducial markers, it is possible to cluster cofactor microenvironments into as few as four major modules: bacterial ferredoxin, cytochrome c, symerythrin and plastocyanin-type folds. From structural alignments, it is challenging to ascertain whether modules evolved from a single common ancestor (homology) or arose by independent convergence on a limited set of structural forms (analogy). Additional insight into common origins is contained in the spatial adjacency network (SPAN), which is based on proximity of modules in oxidoreductases containing multiple cofactor electron transfer chains. Electron transfer chains within complex modern oxidoreductases likely evolved through repeated duplication and diversification of ancient modular units that arose in the Archean eon. [ABSTRACT FROM AUTHOR]

Abstract: Understanding the cellular and molecular responses of stony corals to ocean acidification is key to predicting their ability to calcify under projected high CO2 conditions. Of specific interest are the links between biomineralization proteins and the precipitation of new calcium carbonate (CaCO3), which potentially can provide a better understanding of the biomineralization process. We have assessed the effects of increased CO2 on the calcification process in cell cultures of the stony coral, Stylophora pistillata, reared in nutrient‐enriched artificial seawater at four pCO2 levels and two glucose concentrations. Dispersed S. pistillata cells grown at low (400 ppmV) and moderate (700 ppmV) pCO2 re‐aggregate into proto‐polyps and precipitate CaCO3. When grown at pCO2 levels of 1000 ppmV and 2000 ppmV, the cells up‐regulate genes for two highly acidic proteins as well as a carbonic anhydrase, but down‐regulate long term cadherin protein production and minimize proto‐polyp formation, and exhibit a significant decrease in measurable CaCO3 precipitation. However, cell cultures precipitate CaCO3 in all treatments, even at slightly undersaturated conditions (Ωaragonite < 0.95). Glucose addition does not influence either biomineralization gene expression or calcification rate. Measured δ11B of the mineral phase, as a proxy of the pH at the calcifying sites, is out of equilibrium with the ambient seawater medium surrounding the cells and proto‐polyps, suggesting pH is elevated in the micro‐environment of the precipitating mineral. Our results suggest that coral cells possess molecular mechanisms to help compensate for the effects of ocean acidification within the bounds projected in the coming century. [ABSTRACT FROM AUTHOR]

Constraining photosynthetic energy conversion efficiency in nature is challenging. In principle, two yield measurements must be made simultaneously: photochemistry, fluorescence and/or thermal dissipation. We constructed two different, extremely sensitive and precise active fluorometers: one measures the quantum yield of photochemistry from changes in variable fluorescence, the other measures fluorescence lifetimes in the picosecond time domain. By deploying the pair of instruments on eight transoceanic cruises over six years, we obtained over 200 000 measurements of fluorescence yields and lifetimes from surface waters in five ocean basins. Our results revealed that the average quantum yield of photochemistry was approximately 0.35 while the average quantum yield of fluorescence was approximately 0.07. Thus, closure on the energy budget suggests that, on average, approximately 58% of the photons absorbed by phytoplankton in the world oceans are dissipated as heat. This extraordinary inefficiency is associated with the paucity of nutrients in the upper ocean, especially dissolved inorganic nitrogen and iron. Our results strongly suggest that, in nature, most of the time, most of the phytoplankton community operates at approximately half of its maximal photosynthetic energy conversion efficiency because nutrients limit the synthesis or function of essential components in the photosynthetic apparatus. [ABSTRACT FROM AUTHOR]

The inhibitor NU 2058 [6-(cyclohexylmethoxy)-9H-purin-2-amine] leads to G1-phase cell cycle arrest in the marine diatom, Phaeodactylum tricornutum, by binding to two cyclin-dependent kinases, CDKA1 and CDKA2. NU 2058 has no effect on photosynthetic attributes, such as Fv/Fm, chlorophyll a/cell, levels of D2 PSII subunits, or RbcL; however, cell cycle arrest leads to unbalanced growth whereby photosynthetic products that can no longer be used for cell division are redirected toward carbohydrates and triacylglycerols (TAGs). Arrested cells up-regulate most genes involved in fatty acid synthesis, including acetyl-CoA carboxylase, and three out of five putative type II diglyceride acyltransferases (DGATs), the enzymes that catalyze TAG production. Correlation of transcriptomes in arrested cells with a flux balance model for P. tricornutum predicts that reactions in the mitochondrion that supply glycerate may support TAG synthesis. Our results reveal that sources of intermediate metabolites and macromolecular sinks are tightly coupled to the cell cycle in a marine diatom, and that arresting cells in the G1 phase leads to remodeling of intermediate metabolism and unbalanced growth. [ABSTRACT FROM AUTHOR]

Amundsen Sea polynyas are among the most productive, yet climate-sensitive ecosystems in the Southern Ocean and host massive annual phytoplankton blooms. These blooms are believed to be controlled by iron fluxes from melting ice and icebergs and by intrusion of nutrient-rich Circumpolar Deep Water, however the interplay between iron effects and other controls, such as light availability, has not yet been quantified. Here, we examine phytoplankton photophysiology in relation to Fe stress and physical forcing in two largest polynyas, Amundsen Sea Polynya (ASP) and Pine Island Polynya (PIP), using the combination of high-resolution variable fluorescence measurements, fluorescence lifetime analysis, photosynthetic rates, and Fe-enrichment incubations. These analyses revealed strong Fe stress in the ASP, whereas the PIP showed virtually no signatures of Fe limitation. In spite of enhanced iron availability in the PIP, chlorophyll biomass remained ∼ 30-50% lower than in the Fe-stressed ASP. This apparent paradox would not have been observed if iron were the main control of phytoplankton bloom in the Amundsen Sea. Long-term satellite-based climatology records revealed that the ASP is exposed to significantly higher solar irradiance levels throughout the summer season, as compared to the PIP region, suggesting that light availability controls the magnitude of phytoplankton blooms in the Amundsen Sea. Our data suggests that higher Fe availability (e.g., due to higher melting rates of ice sheets) would not necessarily increase primary productivity in this region. Furthermore, stronger wind-driven vertical mixing in expanding ice-free areas may lead to reduction in light availability and productivity in the future. [ABSTRACT FROM AUTHOR]

We measured the light dependence of gross photosynthesis and oxygen uptake rates by membrane inlet mass spectrometry in two open ocean regions: the Amundsen Sea (Antarctica), dominated by Phaeocystis antarctica, and the North Atlantic, dominated by Emiliania huxleyi. In the North Atlantic, respiration was independent of irradiance and was higher than the gross photosynthetic rate at all irradiances. In contrast, in the Amundsen Sea, oxygen uptake processes were light dependent; dark respiration was one order of magnitude lower than the maximal gross photosynthetic rate, but the oxygen uptake rate increased by 10 fold at surface irradiances. Our results suggest the light dependence of oxygen uptake in Amundsen Sea has two sources: one is independent of photosynthesis, and is possibly associated with the photo-reduction of O2 mediated by dissolved organic matter; the second reflects the activity of an oxidase fueled in the light with photosynthetic electron flow. Our results highlight the importance of improving our understanding of oxygen consuming reactions in the euphotic zone. [ABSTRACT FROM AUTHOR]

Under nutrient deplete conditions, diatoms accumulate between 15% to 25% of their dry weight as lipids, primarily as triacylglycerols ( TAGs). As in most eukaryotes, these organisms produce TAGs via the acyl-CoA dependent Kennedy pathway. The last step in this pathway is catalyzed by diacylglycerol acyltransferase ( DGAT) that acylates diacylglycerol ( DAG) to produce TAG. To test our hypothesis that DGAT plays a major role in controlling the flux of carbon towards lipids, we overexpressed a specific type II DGAT gene, DGAT2D, in the model diatom Phaeodactylum tricornutum. The transformants had 50- to 100-fold higher DGAT2D mRNA levels and the abundance of the enzyme increased 30- to 50-fold. More important, these cells had a 2-fold higher total lipid content and incorporated carbon into lipids more efficiently than the wild type ( WT) while growing only 15% slower at light saturation. Based on a flux analysis using 13C as a tracer, we found that the increase in lipids was achieved via increased fluxes through pyruvate and acetyl-CoA. Our results reveal overexpression of DAGT2D increases the flux of photosynthetically fixed carbon towards lipids, and leads to a higher lipid content than exponentially grown WT cells. [ABSTRACT FROM AUTHOR]

Molybdoenzymes are an ancient protein family found in phylogenetically and ecologically diverse prokaryotes. Under anaerobic conditions, respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that act as terminal electron acceptors for energy generation. Here, we used probe sequences to conduct an extensive genomic survey and phylogenetic inference for NarG, DmsA, TorA and nine other respiratory molybdoenzyme subfamilies. Our analysis demonstrates their abundance in 60% of prokaryotic phyla. In contrast to many other autonomic genetic units in prokaryotes, the major route of evolution of their predominant subfamilies is vertical gene transfer, gene duplication and divergence. Our results show the robustness of genomic co-occurrence of respiratory molybdoenzymes genes, found in the majority of studied species, for most of the enzyme subfamilies. Genomes which encode for multiple respiratory molybdoenzymes are also enriched in genes regulating replication, recombination and mobility of genetic elements. Respiratory molybdoenzymes were found in prokaryotes associated with diverse environments occupying terrestrial, aquatic, food and host-related habitats, emphasizing their essential role in adaptation of prokaryotes to changing environments. Interestingly, host-associated prokaryotes such as human pathogens more frequently carry multiple respiratory molybdoenzyme genes compared with non-host-associated prokaryotes, highlighting the importance of metabolic flexibility in host-microbiome environments. [ABSTRACT FROM AUTHOR]

All life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids-the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena. [ABSTRACT FROM AUTHOR]

Reef-building corals begin as non-calcifying larvae that, upon settling, rapidly begin to accrete skeleton and a protein-rich skeletal organic matrix that attach them to the reef. Here, we characterized the temporal and spatial expression pattern of a suite of biomineralization genes during three stages of larval development in the reef-building coral Pocillopora damicornis: stage I, newly released; stage II, oral-aborally compressed and stage III, settled and calcifying spat. Transcriptome analysis revealed 3882 differentially expressed genes that clustered into four distinctly different patterns of expression change across the three developmental stages. Immunolocalization analysis further reveals the spatial arrangement of coral acid-rich proteins (CARPs) in the overall architecture of the emerging skeleton. These results provide the first analysis of the timing of the biomineralization 'toolkit' in the early life history of a stony coral. [ABSTRACT FROM AUTHOR]

Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms. [ABSTRACT FROM AUTHOR]

When diatoms are stressed for inorganic nitrogen they remodel their intermediate metabolism and redirect carbon towards lipid biosynthesis. However, this response comes at a significant cost reflected in decreased photosynthetic energy conversion efficiency and growth. Here we explore a molecular genetics approach to restrict the assimilation of inorganic nitrogen by knocking down nitrate reductase (NR). The transformant strain, NR21, exhibited about 50% lower expression and activity of the enzyme but simultaneously accumulated over 40% more fatty acids. However, in contrast to nitrogen-stressed wild-type (WT) cells, which grow at about 20% of the rate of nitrogen-replete cells, growth of NR21 was only reduced by about 30%. Biophysical analyses revealed that the photosynthetic energy conversion efficiency of photosystem II was unaffected in NR21; nevertheless, the plastoquinone pool was reduced by 50% at the optimal growth irradiance while in the WT it was over 90% oxidized. Further analyses reveal a 12-fold increase in the glutamate/glutamine ratio and an increase NADPH and malonyl-CoA pool size. Transcriptomic analyses indicate that the knock down resulted in changes in the expression of genes for lipid biosynthesis, as well as the expression of specific transcription factors. Based on these observations, we hypothesize that the allocation of carbon and reductants in diatoms is controlled by a feedback mechanism between intermediate metabolites, the redox state of the plastid and the expression and binding of transcription factors related to stress responses. [ABSTRACT FROM AUTHOR]

Diatoms are one of the most ecologically successful classes of photosynthetic marine eukaryotes in the contemporary oceans. Over the past 30 million years, they have helped to moderate Earth's climate by absorbing carbon dioxide from the atmosphere, sequestering it via the biological carbon pump and ultimately burying organic carbon in the lithosphere. The proportion of planetary primary production by diatoms in the modern oceans is roughly equivalent to that of terrestrial rainforests. In photosynthesis, the efficient conversion of carbon dioxide into organic matter requires a tight control of the ATP/NADPH ratio which, in other photosynthetic organisms, relies principally on a range of plastid-localized ATP generating processes. Here we show that diatoms regulate ATP/NADPH through extensive energetic exchanges between plastids and mitochondria. This interaction comprises the re-routing of reducing power generated in the plastid towards mitochondria and the import of mitochondrial ATP into the plastid, and is mandatory for optimized carbon fixation and growth. We propose that the process may have contributed to the ecological success of diatoms in the ocean. [ABSTRACT FROM AUTHOR]

Marine diatoms are silica-precipitating microalgae that account for over half of organic carbon burial in marine sediments and thus they play a key role in the global carbon cycle. Their evolutionary expansion during the Cenozoic era (66 Ma to present) has been associated with a superior competitive ability for silicic acid relative to other siliceous plankton such as radiolarians, which evolved by reducing the weight of their silica test. Here we use a mathematical model in which diatoms and radiolarians compete for silicic acid to show that the observed reduction in the weight of radiolarian tests is insufficient to explain the rise of diatoms. Using the lithium isotope record of seawater as a proxy of silicate rock weathering and erosion, we calculate changes in the input flux of silicic acid to the oceans. Our results indicate that the long-term massive erosion of continental silicates was critical to the subsequent success of diatoms in marine ecosystems over the last 40 My and suggest an increase in the strength and efficiency of the oceanic biological pump over this period. [ABSTRACT FROM AUTHOR]

Diatoms are unicellular algae that accumulate significant amounts of triacylglycerols as storage lipids when their growth is limited by nutrients. Using biochemical, physiological, bioinformatics, and reverse genetic approaches, we analyzed how the flux of carbon into lipids is influenced by nitrogen stress in a model diatom, Phaeodactylum tricornutum. Our results reveal that the accumulation of lipids is a consequence of remodeling of intermediate metabolism, especially reactions in the tricarboxylic acid and the urea cycles. Specifically, approximately one-half of the cellular proteins are cannibalized; whereas the nitrogen is scavenged by the urea and glutamine synthetase/glutamine 2-oxoglutarate aminotransferase pathways and redirected to the de novo synthesis of nitrogen assimilation machinery, simultaneously, the photobiological flux of carbon and reductants is used to synthesize lipids. Tofurther examine how nitrogen stress triggers the remodeling process, we knocked down the gene encoding for nitrate reductase, a key enzyme required for the assimilation of nitrate. The strain exhibits 40-50% of the mRNA copy numbers, protein content, and enzymatic activity of the wild type, concomitant with a 43% increase in cellular lipid content. We suggest a negative feedback sensor that couples photosynthetic carbon fixation to lipid biosynthesis and is regulated by the nitrogen assimilation pathway. This metabolic feedback enables diatoms to rapidly respond tofluctuations in environmental nitrogen availability. [ABSTRACT FROM AUTHOR]

The precipitation and assembly of calcium carbonate skeletons by stony corals is a precisely controlled process regulated by the secretion of an ECM. Recently, it has been reported that the proteome of the skeletal organic matrix (SOM) contains a group of coral acid-rich proteins as well as an assemblage of adhesion and structural proteins, which together, create a framework for the precipitation of aragonite. To date, we are aware of no report that has investigated the localization of individual SOM proteins in the skeleton. In particular, no data are available on the ultrastructural mapping of these proteins in the calcification site or the skeleton. This information is crucial to assessing the role of these proteins in biomineralization. Immunological techniques represent a valuable approach to localize a single component within a calcified skeleton. By using immunogold labeling and immunohistochemical assays, here we show the spatial arrangement of key matrix proteins in tissue and skeleton of the common zooxanthellate coral, Stylophora pistillata. To our knowledge, our results reveal for the first time that, at the nanoscale, skeletal proteins are embedded within the aragonite crystals in a highly ordered arrangement consistent with a diel calcification pattern. In the tissue, these proteins are not restricted to the calcifying epithelium, suggesting that they also play other roles in the coral's metabolic pathways. [ABSTRACT FROM AUTHOR]

Oxidoreductases mediate electron transfer (i.e., redox) reactions across the tree of life and ultimately facilitate the biologically driven fluxes of hydrogen, carbon, nitrogen, oxygen, and sulfur on Earth. The core enzymes responsible for these reactions are ancient, often small in size, and highly diverse in amino acid sequence, and many require specific transition metals in their active sites. Here we reconstruct the evolution of metal-binding domains in extant oxidoreductases using a flexible network approach and permissive profile alignments based on available microbial genome data. Our results suggest there were at least 10 independent origins of redox domain families. However, we also identified multiple ancient connections between Fe2S2- (adrenodoxin-like) and heme- (cytochrome c) binding domains. Our results suggest that these two iron-containing redox families had a single common ancestor that underwent duplication and divergence. The iron-containing protein family constitutes ~50% of all metal-containing oxidoreductases and potentially catalyzed redox reactions in the Archean oceans. Heme-binding domains seem to be derived viamodular evolutionary processes that ultimately formthe backbone of redox reactions in both anaerobic and aerobic respiration and photosynthesis. The empirically discovered network allows us to peer into the ancient history of microbial metabolism on our planet. [ABSTRACT FROM AUTHOR]

Diatoms, unicellular phytoplankton that account for ∼40% of marine primary productivity, often dominate coastal and open-ocean upwelling zones. Limitation of growth and productivity by iron at low light is attributed to an elevated cellular Fe requirement for the synthesis of Fe-rich photosynthetic proteins. In the dynamic coastal environment, Fe concentrations and daily surface irradiance levels can vary by two to three orders of magnitude on short spatial and temporal scales. Although genome-wide studies are beginning to provide insight into the molecular mechanisms used by diatoms to rapidly respond to such fluxes, their functional role in mediating the Fe stress response remains uncharacterized. Here, we show, using reverse genetics, that a death-specific protein (DSP; previously named for its apparent association with cell death) in the coastal diatom Thalassiosira pseudonana (TpDSP1) localizes to the plastid and enhances growth during acute Fe limitation at subsaturating light by increasing the photosynthetic efficiency of carbon fixation. Clone lines overexpressing TpDSP1 had a lower quantum requirement for growth, increased levels of photosynthetic and carbon fixation proteins, and increased cyclic electron flow around photosystem I. Cyclic electron flow is an ATPproducing pathway essential in higher plants and chlorophytes with a heretofore unappreciated role in diatoms. However, cells under replete conditions were characterized as having markedly reduced growth and photosynthetic rates at saturating light, thereby constraining the benefits afforded by overexpression. Widespread distribution of DSP-like sequences in environmental metagenomic and metatranscriptomic datasets highlights the presence and relevance of this protein in natural phytoplankton populations in diverse oceanic regimes. [ABSTRACT FROM AUTHOR]

Oxidoreductases play a central role in catalysing enzymatic electron-transfer reactions across the tree of life. To first order, the equilibrium thermodynamic properties of these proteins are governed by protein folds associated with specific transition metals and ligands at the active site. A global analysis of holoenzyme structures and functions suggests that there are fewer than approximately 500 fundamental oxidoreductases, which can be further clustered into 35 unique groups. These catalysts evolved in prokaryotes early in the Earth's history and are largely responsible for the emergence of non-equilibrium biogeochemical cycles on the planet's surface. Although the evolutionary history of the amino acid sequences in the oxidoreductases is very difficult to reconstruct due to gene duplication and horizontal gene transfer, the evolution of the folds in the catalytic sites can potentially be used to infer the history of these enzymes. Using a novel, yet simple analysis of the secondary structures associated with the ligands in oxidoreductases, we developed a structural phylogeny of these enzymes. The results of this 'composome' analysis suggest an early split from a basal set of a small group of proteins dominated by loop structures into two families of oxidoreductases, one dominated by a-helices and the second by β-sheets. The structural evolutionary patterns in both clades trace redox gradients and increased hydrogen bond energy in the active sites. The overall pattern suggests that the evolution of the oxidoreductases led to decreased entropy in the transition metal folds over approximately 2.5 billion years, allowing the enzymes to use increasingly oxidized substrates with high specificity. [ABSTRACT FROM AUTHOR]

Photochemical reactions of minerals are underappreciated processes that can make or break chemical bonds. We report the photooxidation of siderite (FeCO3) by UV radiation to produce hydrogen gas and iron oxides via a two-photon reaction. The calculated quantum yield for the reaction suggests photooxidation of siderite would have been a significant source of molecular hydrogen for the first half of Earth's history. Further, experimental results indicate this abiotic, photochemical process may have led to the formation of iron oxides under anoxic conditions. The reaction would have continued through the Archean to at least the early phases of the Great Oxidation Event, and provided a mechanism for oxidizing the atmosphere through the loss of hydrogen to space, while simultaneously providing a key reductant for microbial metabolism. We propose that the photochemistry of Earth-abundant minerals with wide band gaps would have potentially played a critical role in shaping the biogeochemical evolution of early Earth. [ABSTRACT FROM AUTHOR]

We determined the quantum requirements for growth (1/ϕμ) and fatty acid ( FA) biosynthesis (1/ϕFA) in the marine diatom, Phaeodactylum tricornutum, grown in nutrient replete conditions with nitrate or ammonium as nitrogen sources, and under nitrogen limitation, achieved by transferring cells into nitrogen free medium or by inhibiting nitrate assimilation with tungstate. A treatment in which tungstate was supplemented to cells grown with ammonium was also included. In nutrient replete conditions, cells grew exponentially and possessed virtually identical 1/ϕμ of 40-44 mol photons · mol C−1. In parallel, 1/ϕFA varied between 380 and 409 mol photons · mol C−1 in the presence of nitrate, but declined to 348 mol photons · mol C−1 with ammonium and to 250 mol photons · mol C−1 with ammonium plus tungstate, indicating an increase in the efficiency of FA biosynthesis relative to cells grown on nitrate of 8% and 35%, respectively. While the molecular mechanism for this effect remains poorly understood, the results unambiguously reveal that cells grown on ammonium are able to direct more reductant to lipids. This analysis suggests that when cells are grown with a reduced nitrogen source, fatty acid biosynthesis can effectively become a sink for excess absorbed light, compensating for the absence of energetically demanding nitrate assimilation reactions. Our data further suggest that optimal lipid production efficiency is achieved when cells are in exponential growth, when nitrate assimilation is inhibited, and ammonium is the sole nitrogen source. [ABSTRACT FROM AUTHOR]

It has long been recognized that a suite of proteins exists in coral skeletons that is critical for the oriented precipitation of calcium carbonate crystals, yet these proteins remain poorly characterized. Using liquid chromatography-tandem mass spectrometry analysis of proteins extracted from the cell-free skeleton of the hermatypic coral, Stylophora pistillata, combined with a draft genome assembly from the cnidarian host cells of the same species, we identified 36 coral skeletal organic matrix proteins. The proteome of the coral skeleton contains an assemblage of adhesion and structural proteins as well as two highly acidic proteins that may constitute a unique coral skeletal organic matrix protein subfamily. We compared the 36 skeletal organic matrix protein sequences to genome and transcriptome data from three other corals, three additional invertebrates, one vertebrate, and three single-celled organisms. This work represents a unique extensive proteomic analysis of biomineralization-related proteins in corals from which we identify a biomineralization "toolkit," an organic scaffold upon which aragonite crystals can be deposited in specific orientations to form a phenotypically identifiable structure. [ABSTRACT FROM AUTHOR]

The mechanisms of coral calcification at the molecular, cellular and tissue levels are poorly understood. In this study, we examine calcium carbonate precipitation using novel coral tissue cultures that aggregate to form "proto-polyps". Our goal is to establish an experimental system in which calcification is facilitated at the cellular level, while simultaneously allowing in vitro manipulations of the calcifying fluid. This novel coral culturing technique enables us to study the mechanisms of biomineralization and their implications for geochemical proxies. Viable cell cultures of the hermatypic, zooxanthellate coral, Stylophora pistillata, have been maintained for 6 to 8 weeks. Using an enriched seawater medium with aragonite saturation state similar to open ocean surface waters (Ωarag,4), the primary cell cultures assemble into "proto-polyps" which form an extracellular organic matrix (ECM) and precipitate aragonite crystals. These extracellular aragonite crystals, about 10 mm in length, are formed on the external face of the proto-polyps and are identified by their distinctive elongated crystallography and X-ray diffraction pattern. The precipitation of aragonite is independent of photosynthesis by the zooxanthellae, and does not occur in control experiments lacking coral cells or when the coral cells are poisoned with sodium azide. Our results demonstrate that proto-polyps, aggregated from primary coral tissue culture, function (from a biomineralization perspective) similarly to whole corals. This approach provides a novel tool for investigating the biophysical mechanism of calcification in these organisms. [ABSTRACT FROM AUTHOR]

Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe4S4 metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple &agr;+&bgr; fold is found alone or as a domain in larger proteins throughout all three kingdoms of life. Previous analyses of the heptapeptide conformation in experimentally determined ferredoxin structures revealed a pervasive right-handed topology, despite the fact that the Fe4S4 cluster is achiral. Conformational enumeration of a model CGGCGGC heptapeptide bound to a cubane iron-sulfur cluster indicates both left-handed and right-handed folds could exist and have comparable stabilities. However, only the natural ferredoxin topology provides a significant network of backbone-to-cluster hydrogen bonds that would stabilize the metal-peptide complex. The optimal peptide configuration (alternating &agr;L,&agr;R) is that of an &agr;-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding. INSET: Author Summary. [ABSTRACT FROM AUTHOR]

During the past several decades, numerous reports from disparate geographical areas have documented an increased frequency of "bleaching" in reef-forming corals. The phenomenon, triggered by increased sea surface temperatures, occurs when the cnidarian hosts digest and/or expel their intracellular, photosynthetic dinoflagellate symbionts ("zooxanthellae" in the genus Symbiodinium). Although coral bleaching is often followed by the death of the animal hosts, in some cases, the animal survives and can be repopulated with viable zooxanthellae. The physiological factors determining the ability of the coral. to survive bleaching events are poorly understood. In this study, we experimentally established that bleaching and death of the host animal involve a caspase-mediated apoptotic cascade induced by reactive oxygen species produced primarily by the algal symbionts. In addition, we demonstrate that, although some corals naturally suppress caspase activity and significantly reduce caspase concentration under high temperatures as a mechanism to prevent colony death from apoptosis, even sensitive corals can be prevented from dying by application of exogenous inhibitors of caspases. Our results indicate that variability in response to thermal stress in corals is determined by a four-element, combinatorial genetic matrix intrinsic to the specific symbiotic association. Based on our experimental data, we present a working model in which the phenotypic expression of this symbiont/host relationship places a selective pressure on the symbiotic association. The model predicts the survival of the host animals in which the caspase-mediated apoptotic cascade is down-regulated. [ABSTRACT FROM AUTHOR]

Mesodinium rubrum (= Myrionecta rubra), a marine ciliate, acquires plastids, mitochondria, and nuclei from cryptophyte algae. Using a strain of M. rubrum isolated from McMurdo Sound, Antarctica, we investigated the photoacclimation potential of this trophically unique organism at a range of low irradiance levels. The compensation growth irradiance for M. rubrum was 0.5 μmol quanta · m · s, and growth rate saturated at ∼20 μmol quanta · m · s. The strain displayed trends in photosynthetic efficiency and pigment content characteristic of marine phototrophs. Maximum chl a-specific photosynthetic rates were an order of magnitude slower than temperate strains, while growth rates were half as large, suggesting that a thermal limit to enzyme kinetics produces a fundamental limit to cell function. M. rubrum acclimates to light- and temperature-limited polar conditions and closely regulates photosynthesis in its cryptophyte organelles. By acquiring and maintaining physiologically viable, plastic plastids, M. rubrum establishes a selective advantage over purely heterotrophic ciliates but reduces competition with other phototrophs by exploiting a very low-light niche. [ABSTRACT FROM AUTHOR]

Summary Iron is widely thought to limit nitrogen fixation in the open, oligotrophic ocean due to the low solubility of Fe in oxic seawater and the high Fe demand for the nitrogenase holozyme. However, empirical evidence for Fe limitation of field populations of Trichodesmium based on either incubation experiments or molecular and physiological indicators has not quantitatively related Fe supply to the cellular Fe quotas for nitrogenase. Rather, the Fe required for N2 fixation has been inferred from in vivo catalytic activity. Using a pet14b expression vector, we cloned the nif H gene (encoding the Fe-protein, which contains 4Fe atoms per subunit) from Trichodesmium IMS 101, and purified the His-tagged apoprotein with which we derived a primary standard based on quantitative Western blots. Using a standard curve derived from the cloned Trichodesmium Fe apoprotein, we measured the absolute abundance of the Fe-protein in iron-replete cultures of this marine diazotroph. At peak expression, we calculate 0.04 mg nitrogenase mg−1 C. Assuming a conservative stoichiometry of two Fe-protein subunits per MoFe protein (which contains 15 Fe atoms per subunit, or a total of 38 atoms of Fe per holozyme), we estimate 236 µmol Fe is bound to nitrogenase per mol cellular C. This estimate is about 10 times greater than the Fe previously calculated to support diazotrophic growth under these conditions. Our results suggest that under bloom conditions in the subtropical North Atlantic and North Pacific, as much as ∼2.22 and 0.06 µmol m−3 of Fe is bound to Trichodesmium nitrogenase respectively. Such a high quota represents between ∼50% and > 100% summer-time average particulate Fe in surface waters, suggesting the importance of this taxon for the retention and biogeochemical cycling of Fe. Moderate growth (0.10 day−1) towards the end of these blooms would require a vertical flux as high as ∼23 µmol Fe day−1 m−2 into the mixed layer. [ABSTRACT FROM AUTHOR]