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  • National Academy of Sciences
  • 2010-2014  (14)
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  • 1
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 104 (9). pp. 3037-3042.
    Publication Date: 2019-09-23
    Description: Increased knowledge of the present global carbon cycle is important for our ability to understand and to predict the future carbon cycle and global climate. Approximately half of the anthropogenic carbon released to the atmosphere from fossil fuel burning is stored in the ocean, although distribution and regional fluxes of the ocean sink are debated. Estimates of anthropogenic carbon (C ant) in the oceans remain prone to error arising from (i) a need to estimate preindustrial reference concentrations of carbon for different oceanic regions, and (ii) differing behavior of transient ocean tracers used to infer C ant. We introduce an empirical approach to estimate C ant that circumvents both problems by using measurement of the decadal change of ocean carbon concentrations and the exponential nature of the atmospheric C ant increase. In contrast to prior approaches, the results are independent of tracer data but are shown to be qualitatively and quantitatively consistent with tracer-derived estimates. The approach reveals more C ant in the deep ocean than prior studies; with possible implications for future carbon uptake and deep ocean carbonate dissolution. Our results suggest that this approachs applied on the unprecedented global data archive provides a means of estimating the C ant for large parts of the world's ocean.
    Type: Article , PeerReviewed
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  • 2
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 106 . pp. 20602-20609.
    Publication Date: 2019-09-23
    Description: Throughout Earth's history, the oceans have played a dominant role in the climate system through the storage and transport of heat and the exchange of water and climate-relevant gases with the atmosphere. The ocean's heat capacity is ≈1,000 times larger than that of the atmosphere, its content of reactive carbon more than 60 times larger. Through a variety of physical, chemical, and biological processes, the ocean acts as a driver of climate variability on time scales ranging from seasonal to interannual to decadal to glacial–interglacial. The same processes will also be involved in future responses of the ocean to global change. Here we assess the responses of the seawater carbonate system and of the ocean's physical and biological carbon pumps to (i) ocean warming and the associated changes in vertical mixing and overturning circulation, and (ii) ocean acidification and carbonation. Our analysis underscores that many of these responses have the potential for significant feedback to the climate system. Because several of the underlying processes are interlinked and nonlinear, the sign and magnitude of the ocean's carbon cycle feedback to climate change is yet unknown. Understanding these processes and their sensitivities to global change will be crucial to our ability to project future climate change.
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  • 3
    Publication Date: 2016-10-25
    Description: Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.
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  • 4
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 105 (30). pp. 10438-10443.
    Publication Date: 2016-10-25
    Description: Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by Phaeodactylum tricornutum at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the Thalassiosira pseudonana genome that encode for components of iron capture and uptake mechanisms.
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  • 5
    Publication Date: 2015-07-02
    Description: In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal-bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other's genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal-bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.
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  • 6
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 106 (31). pp. 12788-12793.
    Publication Date: 2016-11-14
    Description: Understanding the ecological impacts of climate change is a crucial challenge of the twenty-first century. There is a clear lack of general rules regarding the impacts of global warming on biota. Here, we present a metaanalysis of the effect of climate change on body size of ectothermic aquatic organisms (bacteria, phyto- and zooplankton, and fish) from the community to the individual level. Using long-term surveys, experimental data and published results, we show a significant increase in the proportion of small-sized species and young age classes and a decrease in size-at-age. These results are in accordance with the ecological rules dealing with the temperature–size relationships (i.e., Bergmann's rule, James' rule and Temperature–Size Rule). Our study provides evidence that reduced body size is the third universal ecological response to global warming in aquatic systems besides the shift of species ranges toward higher altitudes and latitudes and the seasonal shifts in life cycle events.
    Type: Article , PeerReviewed
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  • 7
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 102 (8). pp. 2826-2831.
    Publication Date: 2016-11-14
    Description: Contemporary climate change is characterized both by increasing mean temperature and increasing climate variability such as heat waves, storms, and floods. How populations and communities cope with such climatic extremes is a question central to contemporary ecology and biodiversity conservation. Previous work has shown that species diversity can affect ecosystem functioning and resilience. Here, we show that genotypic diversity can replace the role of species diversity in a species-poor coastal ecosystem, and it may buffer against extreme climatic events. In a manipulative field experiment, increasing the genotypic diversity of the cosmopolitan seagrass Zostera marina enhanced biomass production, plant density, and faunal abundance, despite near-lethal water temperatures due to extreme warming across Europe. Net biodiversity effects were explained by genotypic complementarity rather than by selection of particularly robust genotypes. Positive effects on invertebrate fauna suggest that genetic diversity has second-order effects reaching higher trophic levels. Our results highlight the importance of maintaining genetic as well as species diversity to enhance ecosystem resilience in a world of increasing uncertainty.
    Type: Article , PeerReviewed
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  • 8
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 109 (44). pp. 18192-18197.
    Publication Date: 2019-09-23
    Description: Calcifying echinoid larvae respond to changes in seawater carbonate chemistry with reduced growth and developmental delay. To date, no information exists on how ocean acidification acts on pH homeostasis in echinoderm larvae. Understanding acid–base regulatory capacities is important because intracellular formation and maintenance of the calcium carbonate skeleton is dependent on pH homeostasis. Using H+-selective microelectrodes and the pH-sensitive fluorescent dye BCECF, we conducted in vivo measurements of extracellular and intracellular pH (pHe and pHi) in echinoderm larvae. We exposed pluteus larvae to a range of seawater CO2 conditions and demonstrated that the extracellular compartment surrounding the calcifying primary mesenchyme cells (PMCs) conforms to the surrounding seawater with respect to pH during exposure to elevated seawater pCO2. Using FITC dextran conjugates, we demonstrate that sea urchin larvae have a leaky integument. PMCs and spicules are therefore directly exposed to strong changes in pHe whenever seawater pH changes. However, measurements of pHi demonstrated that PMCs are able to fully compensate an induced intracellular acidosis. This was highly dependent on Na+ and HCO3−, suggesting a bicarbonate buffer mechanism involving secondary active Na+-dependent membrane transport proteins. We suggest that, under ocean acidification, maintained pHi enables calcification to proceed despite decreased pHe. However, this probably causes enhanced costs. Increased costs for calcification or cellular homeostasis can be one of the main factors leading to modifications in energy partitioning, which then impacts growth and, ultimately, results in increased mortality of echinoid larvae during the pelagic life stage.
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  • 9
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 108 (52). E1484-E1490.
    Publication Date: 2016-10-25
    Description: Microbial degradation of substrates to terminal products is commonly understood as a unidirectional process. In individual enzymatic reactions, however, reversibility (reverse reaction and product back flux) is common. Hence, it is possible that entire pathways of microbial degradation are associated with back flux from the accumulating product pool through intracellular intermediates into the substrate pool. We investigated carbon and sulfur back flux during the anaerobic oxidation of methane (AOM) with sulfate, one of the least exergonic microbial catabolic processes known. The involved enzymes must operate not far from the thermodynamic equilibrium. Such an energetic situation is likely to favor product back flux. Indeed, cultures of highly enriched archaeal–bacterial consortia, performing net AOM with unlabeled methane and sulfate, converted label from 14C-bicarbonate and 35S-sulfide to 14C-methane and 35S-sulfate, respectively. Back fluxes reached 5% and 13%, respectively, of the net AOM rate. The existence of catabolic back fluxes in the reverse direction of net reactions has implications for biogeochemical isotope studies. In environments where biochemical processes are close to thermodynamic equilibrium, measured fluxes of labeled substrates to products are not equal to microbial net rates. Detection of a reaction in situ by labeling may not even indicate a net reaction occurring in the direction of label conversion but may reflect the reverse component of a so far unrecognized net reaction. Furthermore, the natural isotopic composition of the substrate and product pool will be determined by both the forward and back flux. This finding may have to be considered in the interpretation of stable isotope records.
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  • 10
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    National Academy of Sciences
    In:  PNAS Proceedings of the National Academy of Sciences of the United States of America, 108 (48). pp. 19276-19281.
    Publication Date: 2019-09-23
    Description: Large-scale transcription profiling via direct cDNA sequencing provides important insights as to how foundation species cope with increasing climatic extremes predicted under global warming. Species distributed along a thermal cline, such as the ecologically important seagrass Zostera marina, provide an opportunity to assess temperature effects on gene expression as a function of their long-term adaptation to heat stress. We exposed a southern and northern European population of Zostera marina from contrasting thermal environments to a realistic heat wave in a common-stress garden. In a fully crossed experiment, eight cDNA libraries, each comprising ∼125 000 reads, were obtained during and after a simulated heat wave, along with nonstressed control treatments. Although gene-expression patterns during stress were similar in both populations and were dominated by classical heat-shock proteins, transcription profiles diverged after the heat wave. Gene-expression patterns in southern genotypes returned to control values immediately, but genotypes from the northern site failed to recover and revealed the induction of genes involved in protein degradation, indicating failed metabolic compensation to high sea-surface temperature. We conclude that the return of gene-expression patterns during recovery provides critical information on thermal adaptation in aquatic habitats under climatic stress. As a unifying concept for ecological genomics, we propose transcriptomic resilience, analogous to ecological resilience, as an important measure to predict the tolerance of individuals and hence the fate of local populations in the face of global warming.
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