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Journal articles on the topic 'Biogeochemical techniques'
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1
Hahn, A., P. Rosén, P. Kliem, C. Ohlendorf, and B. Zolitschka. "Comparative study of infrared techniques for fast biogeochemical sediment analyses." Geochemistry, Geophysics, Geosystems 12, no. 10 (October 2011): n/a. http://dx.doi.org/10.1029/2011gc003686.
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Samuiloviene, Aurelija, Marco Bartoli, Stefano Bonaglia, Ulisse Cardini, Irma Vybernaite-Lubiene, Ugo Marzocchi, Jolita Petkuviene, Tobia Politi, Anastasija Zaiko, and Mindaugas Zilius. "The Effect of Chironomid Larvae on Nitrogen Cycling and Microbial Communities in Soft Sediments." Water 11, no. 9 (September 16, 2019): 1931. http://dx.doi.org/10.3390/w11091931.
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The combination of biogeochemical methods and molecular techniques has the potential to uncover the black-box of the nitrogen (N) cycle in bioturbated sediments. Advanced biogeochemical methods allow the quantification of the process rates of different microbial processes, whereas molecular tools allow the analysis of microbial diversity (16S rRNA metabarcoding) and activity (marker genes and transcripts) in biogeochemical hot-spots such as the burrow wall or macrofauna guts. By combining biogeochemical and molecular techniques, we analyzed the role of tube-dwelling Chironomus plumosus (Insecta, Diptera) larvae on nitrification and nitrate reduction processes in a laboratory experiment with reconstructed sediments. We hypothesized that chironomid larvae stimulate these processes and host bacteria actively involved in N-cycling. Our results suggest that chironomid larvae significantly enhance the recycling of ammonium (80.5 ± 48.7 µmol m−2 h−1) and the production of dinitrogen (420.2 ± 21.4 µmol m−2 h−1) via coupled nitrification–denitrification and the consumption of water column nitrates. Besides creating oxygen microniches in ammonium-rich subsurface sediments via burrow digging and ventilation, chironomid larvae serve as hot-spots of microbial communities involved in N-cycling. The quantification of functional genes showed a significantly higher potential for microbial denitrification and nitrate ammonification in larvae as compared to surrounding sediments. Future studies may further scrutinize N transformation rates associated with intimate macrofaunal–bacteria associations.
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Hutchins, DA, WX Wang, MA Schmidt, and NS Fisher. "Dual-labeling techniques for trace metal biogeochemical investigations in aquatic plankton communities." Aquatic Microbial Ecology 19 (1999): 129–38. http://dx.doi.org/10.3354/ame019129.
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Ward, Ben A., Marjorie A. M. Friedrichs, Thomas R. Anderson, and Andreas Oschlies. "Parameter optimisation techniques and the problem of underdetermination in marine biogeochemical models." Journal of Marine Systems 81, no. 1-2 (April 2010): 34–43. http://dx.doi.org/10.1016/j.jmarsys.2009.12.005.
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Ethier, Danielle M., Christopher J. Kyle, T. Kurt Kyser, and Joseph J. Nocera. "Variability in the growth patterns of the cornified claw sheath among vertebrates: implications for using biogeochemistry to study animal movement." Canadian Journal of Zoology 88, no. 11 (November 2010): 1043–51. http://dx.doi.org/10.1139/z10-073.
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We review the role of biogeochemical signatures, such as stable isotopes and trace elements, in the cornified claw tissue as a means of studying movement and foraging behaviour of vertebrates because this approach is noninvasive and can capture contemporary and historic signatures. Because biogeochemical techniques are still relatively new in studies of animal movement, we are only beginning to understand how the growth patterns of the cornified claw sheath may affect our ability to interpret the biogeochemical signals in these tissues. To move towards resolving this, we review the morphology of the epidermal cornified claw sheath in several taxa that illustrate substantial variation in growth patterns both between taxa and between individual distinct claw regions. For instance, in mammalian claws, deposition of keratinizing cells from the epidermis is nonlinear because the claw tip is composed of old and new cornified epidermal cells, whereas the cornified blade horn covering the claw’s lateral walls is deposited continuously and without assortment, providing unbroken time-series data. We also consider patterns of growth in mammalian hooves, as well as reptilian, avian, and amphibian cornified claw sheaths, and address the need for expanded research in this field. We conclude this synthesis by describing a noninvasive technique for monitoring growth rates in a model mammal, the American badger ( Taxidea taxus (Schreber, 1777)), and provide guidelines for future sampling of claw keratin, which will improve our ability to back-calculate the time of biogeochemical integration into this tissue.
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Smith, Pete, Fabrizio Albanito, Madeleine Bell, Jessica Bellarby, Sergey Blagodatskiy, Arindam Datta, Marta Dondini, et al. "Systems approaches in global change and biogeochemistry research." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1586 (January 19, 2012): 311–21. http://dx.doi.org/10.1098/rstb.2011.0173.
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Systems approaches have great potential for application in predictive ecology. In this paper, we present a range of examples, where systems approaches are being developed and applied at a range of scales in the field of global change and biogeochemical cycling. Systems approaches range from Bayesian calibration techniques at plot scale, through data assimilation methods at regional to continental scales, to multi-disciplinary numerical model applications at country to global scales. We provide examples from a range of studies and show how these approaches are being used to address current topics in global change and biogeochemical research, such as the interaction between carbon and nitrogen cycles, terrestrial carbon feedbacks to climate change and the attribution of observed global changes to various drivers of change. We examine how transferable the methods and techniques might be to other areas of ecosystem science and ecology.
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Rennert, Thilo, Kai U. Totsche, Katja Heister, Michael Kersten, and Jürgen Thieme. "Advanced spectroscopic, microscopic, and tomographic characterization techniques to study biogeochemical interfaces in soil." Journal of Soils and Sediments 12, no. 1 (August 30, 2011): 3–23. http://dx.doi.org/10.1007/s11368-011-0417-5.
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Chen, X. D., K. E. Dunfield, T. D. Fraser, S. A. Wakelin, A. E. Richardson, and L. M. Condron. "Soil biodiversity and biogeochemical function in managed ecosystems." Soil Research 58, no. 1 (2020): 1. http://dx.doi.org/10.1071/sr19067.
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A complex combination of environmental, biological, chemical, and physical properties and processes determine soil biodiversity and its relationship to biogeochemical functions and ecosystem services. Vegetation, land-use, and land management, in turn, influence diversity and function in the soil ecosystem. The objective of this review was to assess how different land-use systems (crop production, animal production, and planted forest) affect soil biodiversity, and how consequent changes in soil biodiversity influence energy (carbon) and nutrient dynamics. Deficiencies in understanding relationships between soil biodiversity and biogeochemical function in managed ecosystems are highlighted, along with the need to investigate how diversity influences specific processes across different functional groups and trophic levels. The continued development and application of molecular techniques and data informatics with descriptive approaches will contribute to advancing our understanding of soil biodiversity and function in managed agricultural and forest ecosystems.
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Hill, J., E. E. Popova, D. A. Ham, M. D. Piggott, and M. Srokosz. "Adapting to life: ocean biogeochemical modelling and adaptive remeshing." Ocean Science 10, no. 3 (May 9, 2014): 323–43. http://dx.doi.org/10.5194/os-10-323-2014.
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Abstract. An outstanding problem in biogeochemical modelling of the ocean is that many of the key processes occur intermittently at small scales, such as the sub-mesoscale, that are not well represented in global ocean models. This is partly due to their failure to resolve sub-mesoscale phenomena, which play a significant role in vertical nutrient supply. Simply increasing the resolution of the models may be an inefficient computational solution to this problem. An approach based on recent advances in adaptive mesh computational techniques may offer an alternative. Here the first steps in such an approach are described, using the example of a simple vertical column (quasi-1-D) ocean biogeochemical model. We present a novel method of simulating ocean biogeochemical behaviour on a vertically adaptive computational mesh, where the mesh changes in response to the biogeochemical and physical state of the system throughout the simulation. We show that the model reproduces the general physical and biological behaviour at three ocean stations (India, Papa and Bermuda) as compared to a high-resolution fixed mesh simulation and to observations. The use of an adaptive mesh does not increase the computational error, but reduces the number of mesh elements by a factor of 2–3. Unlike previous work the adaptivity metric used is flexible and we show that capturing the physical behaviour of the model is paramount to achieving a reasonable solution. Adding biological quantities to the adaptivity metric further refines the solution. We then show the potential of this method in two case studies where we change the adaptivity metric used to determine the varying mesh sizes in order to capture the dynamics of chlorophyll at Bermuda and sinking detritus at Papa. We therefore demonstrate that adaptive meshes may provide a suitable numerical technique for simulating seasonal or transient biogeochemical behaviour at high vertical resolution whilst minimising the number of elements in the mesh. More work is required to move this to fully 3-D simulations.
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Hill, J., E. E. Popova, D. A. Ham, M. D. Piggott, and M. Srokosz. "Adapting to life: ocean biogeochemical modelling and adaptive remeshing." Ocean Science Discussions 10, no. 6 (November 5, 2013): 1997–2051. http://dx.doi.org/10.5194/osd-10-1997-2013.
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Abstract. An outstanding problem in biogeochemical modelling of the ocean is that many of the key processes occur intermittently at small scales, such as the sub-mesoscale, that are not well represented in global ocean models. As an example, state-of-the-art models give values of primary production approximately two orders of magnitude lower than those observed in the ocean's oligotrophic gyres, which cover a third of the Earth's surface. This is partly due to their failure to resolve sub-mesoscale phenomena, which play a significant role in nutrient supply. Simply increasing the resolution of the models may be an inefficient computational solution to this problem. An approach based on recent advances in adaptive mesh computational techniques may offer an alternative. Here the first steps in such an approach are described, using the example of a~simple vertical column (quasi 1-D) ocean biogeochemical model. We present a novel method of simulating ocean biogeochemical behaviour on a vertically adaptive computational mesh, where the mesh changes in response to the biogeochemical and physical state of the system throughout the simulation. We show that the model reproduces the general physical and biological behaviour at three ocean stations (India, Papa and Bermuda) as compared to a high-resolution fixed mesh simulation and to observations. The simulations capture both the seasonal and inter-annual variations. The use of an adaptive mesh does not increase the computational error, but reduces the number of mesh elements by a factor of 2–3, so reducing computational overhead. We then show the potential of this method in two case studies where we change the metric used to determine the varying mesh sizes in order to capture the dynamics of chlorophyll at Bermuda and sinking detritus at Papa. We therefore demonstrate adaptive meshes may provide a~suitable numerical technique for simulating seasonal or transient biogeochemical behaviour at high spatial resolution whilst minimising computational cost.
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Cristea, Oana Diana, Valentin Vlăduţ, Nicoleta Ungureanu, Diana Lorena Popa, Simona Isticioaia, Liliana Dumitrescu, Gheorghe Matei, and Livia Apostol. "Research on methods, techniques and technologies of carbon sequestration in soil." E3S Web of Conferences 180 (2020): 03021. http://dx.doi.org/10.1051/e3sconf/202018003021.
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Soil is one of the natural reservoirs of the carbon biogeochemical cycle, incorporating approximately 6000 billion tons of carbon. Given that with the industrial development more and more carbon is emitted into the atmosphere, solutions, technologies and methods are being sought to reduce this carbon or, where appropriate, it is not eliminated into the atmosphere. The purpose of this paper is to study and identify the simplest methods to be applied in agriculture, for soil processing, by identifying the techniques, technologies and equipment to achieve this without turning the furrow, so that the carbon incorporated in the soil by plants remains sequestered there.
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Ermakov, V. V., S. F. Tyutikov, and V. N. Danilova. "Ecological Monitoring of the Unal Depression, Northern Ossetiya–Alania, Using Techniques of Biogeochemical Indication." Geochemistry International 58, no. 3 (March 2020): 332–41. http://dx.doi.org/10.1134/s0016702920030040.
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Zehr, J. P., I. Hewson, and P. Moisander. "Molecular biology techniques and applications for ocean sensing." Ocean Science 5, no. 2 (May 8, 2009): 101–13. http://dx.doi.org/10.5194/os-5-101-2009.
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Abstract. The study of marine microorganisms using molecular biological techniques is now widespread in the ocean sciences. These techniques target nucleic acids which record the evolutionary history of microbes, and encode for processes which are active in the ocean today. Molecular techniques can form the basis of remote instrumentation sensing technologies for marine microbial diversity and ecological function. Here we review some of the most commonly used molecular biological techniques. These techniques include the polymerase chain reaction (PCR) and reverse-transcriptase PCR, quantitative PCR, whole assemblage "fingerprinting" approaches (based on nucleic acid sequence or length heterogeneity), oligonucleotide microarrays, and high-throughput shotgun sequencing of whole genomes and gene transcripts, which can be used to answer biological, ecological, evolutionary and biogeochemical questions in the ocean sciences. Moreover, molecular biological approaches may be deployed on ocean sensor platforms and hold promise for tracking of organisms or processes of interest in near-real time.
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Zehr, J. P., I. Hewson, and P. H. Moisander. "Molecular biology techniques and applications for ocean sensing." Ocean Science Discussions 5, no. 4 (November 27, 2008): 625–57. http://dx.doi.org/10.5194/osd-5-625-2008.
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Abstract. The study of marine microorganisms using molecular biological techniques is now widespread in the ocean sciences. These techniques target nucleic acids which record the evolutionary history of microbes, and encode for processes which are active in the ocean today. Here we review some of the most commonly used molecular biological techniques. Molecular biological techniques permit study of the abundance, distribution, diversity, and physiology of microorganisms in situ. These techniques include the polymerase chain reaction (PCR) and reverse-transcriptase PCR, quantitative PCR, whole assemblage "fingerprinting" approaches (based on nucleic acid sequence or length heterogeneity), oligonucleotide microarrays, and high-throughput shotgun sequencing of whole genomes and gene transcripts, which can be used to answer biological, ecological, evolutionary and biogeochemical questions in the ocean sciences. Moreover, molecular biological approaches may be deployed on ocean sensor platforms and hold promise for tracking of organisms or processes of interest in near-real time.
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Bouwman, A. F., M. F. P. Bierkens, J. Griffioen, M. M. Hefting, J. J. Middelburg, H. Middelkoop, and C. P. Slomp. "Nutrient dynamics, transfer and retention along the aquatic continuum from land to ocean: towards integration of ecological and biogeochemical models." Biogeosciences 10, no. 1 (January 2, 2013): 1–22. http://dx.doi.org/10.5194/bg-10-1-2013.
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Abstract. In river basins, soils, groundwater, riparian zones and floodplains, streams, rivers, lakes and reservoirs act as successive filters in which the hydrology, ecology and biogeochemical processing are strongly coupled and together act to retain a significant fraction of the nutrients transported. This paper compares existing river ecology concepts with current approaches to describe river biogeochemistry, and assesses the value of these concepts and approaches for understanding the impacts of interacting global change disturbances on river biogeochemistry. Through merging perspectives, concepts, and modeling techniques, we propose integrated model approaches that encompass both aquatic and terrestrial components in heterogeneous landscapes. In this model framework, existing ecological and biogeochemical concepts are extended with a balanced approach for assessing nutrient and sediment delivery, on the one hand, and nutrient in-stream retention on the other hand.
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Fenton, GE, and SA Short. "Fish age validation by Radiometric analysis of Otoliths." Marine and Freshwater Research 43, no. 5 (1992): 913. http://dx.doi.org/10.1071/mf9920913.
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Radiochemical analysis of aragonitic fish otoliths provides a useful approach to validating ages obtained by more common methods. The history of applications of radiometry using short-lived natural isotopes to clams, Nautilus, living corals and fish otoliths is briefly reviewed. The biogeochemical assumptions required for successful use of these techniques are discussed, and the appropriate mathematical treatments required for data analysis are outlined. Novel normalization techniques designed to widen the validity of this approach are proposed. Desirable lines of further research are also briefly discussed.
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Sun, Zhigao, Xiaojie Mou, Xinhua Li, Lingling Wang, Hongli Song, and Huanhuan Jiang. "Application of stable isotope techniques in studies of carbon and nitrogen biogeochemical cycles of ecosystem." Chinese Geographical Science 21, no. 2 (March 22, 2011): 129–48. http://dx.doi.org/10.1007/s11769-011-0453-5.
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Mattern, Jann Paul, and Christopher A. Edwards. "Simple parameter estimation for complex models — Testing evolutionary techniques on 3-dimensional biogeochemical ocean models." Journal of Marine Systems 165 (January 2017): 139–52. http://dx.doi.org/10.1016/j.jmarsys.2016.10.012.
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Schippers, Axel, and Dagmar Kock. "Geomicrobiology of Sulfidic Mine Dumps: A Short Review." Advanced Materials Research 71-73 (May 2009): 37–41. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.37.
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The geomicrobiology of sulfidic mine dumps is reviewed. More than 30 microbiological studies of sulfidic mine dumps have been published. Mainly culturing approaches such as most probable number (MPN) or agar plates were used to study the microbial communities. More recently, molecular biological techniques such as FISH, CARD-FISH, Q-PCR, T-RFLP, DGGE, or cloning have been applied to quantify microorganisms and to investigate the microbial diversity. Aerobic Fe(II)- and sulfur compound oxidizing microorganisms oxidize pyrite, pyrrhotite and other metal sulfides and play an important role in the formation of acid mine drainage (AMD). Anaerobic microorganisms such as Fe(III)-reducing microorganisms dissolve Fe(III)(hydr)oxides and may thereby release adsorbed or precipitated metals. Sulfate-reducing microorganisms precipitate and immobilize metals. In addition to the microbial communities several biogeochemical processes have been analyzed in mine dumps. Pyrite or pyrrhotite oxidation rates have been measured by different techniques: Column experiments, humidity cells, microcalorimetry, or oxygen consumption measurements. Analyses of stable isotopes of iron, oxygen and sulfur have yielded valuable information on biogeochemical reactions. The microbiology and the biogeochemical processes in sulfidic mine dumps have to be understood for control and prevention of AMD generation and to provide different possibilities for remediation concepts. Today, remediation measures, e.g. under water storage of the waste or covering of the dumps, focus on the inhibition of pyrite oxidation to keep the toxic compounds inside the mine waste dumps. As an alternative to the inhibition of pyrite oxidation, metals which also have economic value could be extracted from mine dumps by the application of different metal extraction technologies including bioleaching.
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Tercier-Waeber, Mary-Lou, and Martial Taillefert. "Remote in situ voltammetric techniques to characterize the biogeochemical cycling of trace metals in aquatic systems." J. Environ. Monit. 10, no. 1 (2008): 30–54. http://dx.doi.org/10.1039/b714439n.
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Chica-Olmo, M., F. Rodriguez, F. Abarca, J. P. Rigol-Sanchez, E. deMiguel, J. A. Gomez, and A. Fernandez-Palacios. "Integrated remote sensing and GIS techniques for biogeochemical characterization of the Tinto-Odiel estuary system, SW Spain." Environmental Geology 45, no. 6 (April 1, 2004): 834–42. http://dx.doi.org/10.1007/s00254-003-0943-6.
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Telszewski, M., A. Chazottes, U. Schuster, A. J. Watson, C. Moulin, D. C. E. Bakker, M. González-Dávila, et al. "Estimating the monthly <i>p</i>CO<sub>2</sub> distribution in the North Atlantic using a self-organizing neural network." Biogeosciences 6, no. 8 (August 5, 2009): 1405–21. http://dx.doi.org/10.5194/bg-6-1405-2009.
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Abstract. Here we present monthly, basin-wide maps of the partial pressure of carbon dioxide (pCO2) for the North Atlantic on a 1° latitude by 1° longitude grid for years 2004 through 2006 inclusive. The maps have been computed using a neural network technique which reconstructs the non-linear relationships between three biogeochemical parameters and marine pCO2. A self organizing map (SOM) neural network has been trained using 389 000 triplets of the SeaWiFS-MODIS chlorophyll-a concentration, the NCEP/NCAR reanalysis sea surface temperature, and the FOAM mixed layer depth. The trained SOM was labelled with 137 000 underway pCO2 measurements collected in situ during 2004, 2005 and 2006 in the North Atlantic, spanning the range of 208 to 437 μatm. The root mean square error (RMSE) of the neural network fit to the data is 11.6 μatm, which equals to just above 3 per cent of an average pCO2 value in the in situ dataset. The seasonal pCO2 cycle as well as estimates of the interannual variability in the major biogeochemical provinces are presented and discussed. High resolution combined with basin-wide coverage makes the maps a useful tool for several applications such as the monitoring of basin-wide air-sea CO2 fluxes or improvement of seasonal and interannual marine CO2 cycles in future model predictions. The method itself is a valuable alternative to traditional statistical modelling techniques used in geosciences.
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Telszewski, M., A. Chazottes, U. Schuster, A. J. Watson, C. Moulin, D. C. E. Bakker, M. González-Dávila, et al. "Estimating the monthly <i>p</i>CO<sub>2</sub> distribution in the North Atlantic using a self-organizing neural network." Biogeosciences Discussions 6, no. 2 (March 30, 2009): 3373–414. http://dx.doi.org/10.5194/bgd-6-3373-2009.
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Abstract. Here we present monthly, basin-wide maps of the partial pressure of carbon dioxide (pCO2) for the North Atlantic on a 1° latitude by 1° longitude grid for years 2004 through 2006 inclusive, constructed using a neural network technique which reconstructs the non-linear relationships between 3 biogeochemical parameters and marine pCO2. A self organizing map (SOM) neural network has been trained using the SeaWiFS-MODIS chlorophyll a concentration, the NCEP/NCAR reanalysis sea surface temperature, and the FOAM mixed layer depth. 389 000 such triplets were used. The trained SOM was labelled with 137 000 underway pCO2 measurements collected in situ during 2004, 2005 and 2006 in the North Atlantic, which span the range of 208 and 437 μatm. The root mean square (RMS) deviation of the neural network fits from the data is 11.55 μatm, which equals to just above 3 per cent of an average pCO2 value in the in situ dataset. The seasonal pCO2 cycle as well as the interannual variability estimates in the major biogeochemical provinces is presented and spatial and temporal variability of the estimated fields is discussed. High resolution combined with basin-wide cover makes the maps a useful tool for several applications such as monitoring of basin-wide air-sea CO2 fluxes or improvement of seasonal and interannual marine CO2 cycles in future model predictions. The method itself is a valuable alternative to traditional statistical modelling techniques used in geosciences.
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Louca, Stilianos, Alyse K. Hawley, Sergei Katsev, Monica Torres-Beltran, Maya P. Bhatia, Sam Kheirandish, Céline C. Michiels, et al. "Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone." Proceedings of the National Academy of Sciences 113, no. 40 (September 21, 2016): E5925—E5933. http://dx.doi.org/10.1073/pnas.1602897113.
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Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet—a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite “leakage” during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.
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Poulson, Simon R., and Annett B. Sullivan. "Assessment of diel chemical and isotopic techniques to investigate biogeochemical cycles in the upper Klamath River, Oregon, USA." Chemical Geology 269, no. 1-2 (January 2010): 3–11. http://dx.doi.org/10.1016/j.chemgeo.2009.05.016.
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Moore, C., A. Barnard, P. Fietzek, M. R. Lewis, H. M. Sosik, S. White, and O. Zielinski. "Optical tools for ocean monitoring and research." Ocean Science 5, no. 4 (December 10, 2009): 661–84. http://dx.doi.org/10.5194/os-5-661-2009.
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Abstract. Requirements for understanding the relationships between ocean color and suspended and dissolved materials within the water column, and a rapidly emerging photonics and materials technology base for performing optical based analytical techniques have generated a diverse offering of commercial sensors and research prototypes that perform optical measurements in water. Through inversion, these tools are now being used to determine a diverse set of related biogeochemical and physical parameters. Techniques engaged include measurement of the solar radiance distribution, absorption, scattering, stimulated fluorescence, flow cytometry, and various spectroscopy methods. Selective membranes and other techniques for material isolation further enhance specificity, leading to sensors for measurement of dissolved oxygen, methane, carbon dioxide, common nutrients and a variety of other parameters. Scientists are using these measurements to infer information related to an increasing set of parameters and wide range of applications over relevant scales in space and time.
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Moore, C., A. Barnard, P. Fietzek, M. R. Lewis, H. M. Sosik, S. White, and O. Zielinski. "Optical tools for ocean monitoring and research." Ocean Science Discussions 5, no. 4 (November 27, 2008): 659–717. http://dx.doi.org/10.5194/osd-5-659-2008.
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Abstract. Requirements for understanding the relationships between ocean color and suspended and dissolved materials within the water column, and a rapidly emerging photonics and materials technology base for performing optical based analytical techniques have generated a diverse offering of commercial sensors and research prototypes that perform optical measurements in water. Through inversion, these tools are now being used to determine a diverse set of related biogeochemical and physical parameters. Techniques engaged include measurement of the solar radiance distribution, absorption, scattering, stimulated fluorescence, flow cytometry, and various spectroscopy methods. Selective membranes and other techniques for material isolation further enhance specificity, leading to sensors for measurement of dissolved oxygen, methane, carbon dioxide, common nutrients and a variety of other parameters. Scientists are using these measurements to infer information related to an increasing set of parameters and wide range of applications over relevant scales in space and time.
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Cinta Pinzaru, Simona, Mircea Ardeleanu, Ioana Brezestean, Fran Nekvapil, and Monica M. Venter. "Biogeochemical specificity of adjacent natural carbonated spring waters from Swiss Alps promptly revealed by SERS and Raman technology." Analytical Methods 11, no. 6 (2019): 800–812. http://dx.doi.org/10.1039/c8ay02580k.
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Inorganic anion content, sediment and microbiomecould be simultaneously assessed in natural carbonated waters combining Raman spectroscopy techniques. The mineral waters provided SERS signature characteristic to cyanobacteria and induced aggregation of the AgNps, that was time dependent and spring specific.
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Garcia-Robledo, Emilio, Cory C. Padilla, Montserrat Aldunate, Frank J. Stewart, Osvaldo Ulloa, Aurélien Paulmier, Gerald Gregori, and Niels Peter Revsbech. "Cryptic oxygen cycling in anoxic marine zones." Proceedings of the National Academy of Sciences 114, no. 31 (July 17, 2017): 8319–24. http://dx.doi.org/10.1073/pnas.1619844114.
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Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30–50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteriaProchlorococcusspp. Free O2levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.
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Letscher, R. T., J. K. Moore, Y. C. Teng, and F. Primeau. "Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model." Biogeosciences 12, no. 1 (January 12, 2015): 209–21. http://dx.doi.org/10.5194/bg-12-209-2015.
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Abstract. Dissolved organic matter (DOM) plays an important role in the ocean's biological carbon pump by providing an advective/mixing pathway for ~ 20% of export production. DOM is known to have a stoichiometry depleted in nitrogen (N) and phosphorus (P) compared to the particulate organic matter pool, a fact that is often omitted from biogeochemical ocean general circulation models. However the variable C : N : P stoichiometry of DOM becomes important when quantifying carbon export from the upper ocean and linking the nutrient cycles of N and P with that of carbon. Here we utilize recent advances in DOM observational data coverage and offline tracer-modeling techniques to objectively constrain the variable production and remineralization rates of the DOM C : N : P pools in a simple biogeochemical-ocean model of DOM cycling. The optimized DOM cycling parameters are then incorporated within the Biogeochemical Elemental Cycling (BEC) component of the Community Earth System Model (CESM) and validated against the compilation of marine DOM observations. The optimized BEC simulation including variable DOM C : N : P cycling was found to better reproduce the observed DOM spatial gradients than simulations that used the canonical Redfield ratio. Global annual average export of dissolved organic C, N, and P below 100 m was found to be 2.28 Pg C yr−1 (143 Tmol C yr−1, 16.4 Tmol N yr−1, and 1 Tmol P yr−1, respectively, with an average export C : N : P stoichiometry of 225 : 19 : 1 for the semilabile (degradable) DOM pool. Dissolved organic carbon (DOC) export contributed ~ 25% of the combined organic C export to depths greater than 100 m.
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Letscher, R. T., J. K. Moore, Y. C. Teng, and F. Primeau. "Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model." Biogeosciences Discussions 11, no. 6 (June 16, 2014): 9071–101. http://dx.doi.org/10.5194/bgd-11-9071-2014.
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Abstract. Dissolved organic matter (DOM) plays an important role in the ocean's biological carbon pump by providing an advective/mixing pathway for ~ 20% of export production. DOM is known to have a stoichiometry depleted in nitrogen (N) and phosphorus (P) compared to the particulate organic matter pool, a~fact that is often omitted from biogeochemical-ocean general circulation models. However the variable C : N : P stoichiometry of DOM becomes important when quantifying carbon export from the upper ocean and linking the nutrient cycles of N and P with that of carbon. Here we utilize recent advances in DOM observational data coverage and offline tracer-modeling techniques to objectively constrain the variable production and remineralization rates of the DOM C / N / P pools in a simple biogeochemical-ocean model of DOM cycling. The optimized DOM cycling parameters are then incorporated within the Biogeochemical Elemental Cycling (BEC) component of the Community Earth System Model and validated against the compilation of marine DOM observations. The optimized BEC simulation including variable DOM C : N : P cycling was found to better reproduce the observed DOM spatial gradients than simulations that used the canonical Redfield ratio. Global annual average export of dissolved organic C, N, and P below 100 m was found to be 2.28 Pg C yr−1 (143 Tmol C yr−1), 16.4 Tmol N yr−1, and 1 Tmol P yr−1, respectively with an average export C : N : P stoichiometry of 225 : 19 : 1 for the semilabile (degradable) DOM pool. DOC export contributed ~ 25% of the combined organic C export to depths greater than 100 m.
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Lien, Po Jen, Hsiao Jung Ho, Tzu Hsin Lee, Wen Liang Lai, and Chih Ming Kao. "Effects of Aquifer Heterogeneity and Geochemical Variation on Petroleum-Hydrocarbon Biodegradation at a Gasoline Spill Site." Advanced Materials Research 1079-1080 (December 2014): 584–88. http://dx.doi.org/10.4028/www.scientific.net/amr.1079-1080.584.
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In subsurface environment, small-scale heterogeneities usually cause the reduction of the applicability of in situ remedial techniques. Biogeochemical heterogeneities and preferential groundwater flow paths create complex hydrogeologic conditions at most contaminated sites. A thorough understanding of the resulting three-dimensional distribution of contaminants is a necessity prior to determining a need for remediation. In this study, a gasoline spill site was selected to examine the effects of aquifer heterogeneities and geochemical variations on petroleum hydrocarbon biodegradation via different oxidation-reduction process. At this site, two multilevel sampling wells were installed to delineate the lateral (5 m) and vertical (0.5 m) distribution of contaminant concentrations and different biogeochemical parameters. Two 5-cm (I.D.) continuous soil cores [from 4 to 8 m below land surface (bls)] were collected within the gasoline plume to evaluate the distribution of the microbial population in soils. Results show that high microbial activities were observed in soil samples based on the following evidences: (1) high petroleum hydrocarbon degradation rate, and (2) high microbial biomass. Each soil section was used for chemical extraction, microbial enumeration, and grain size distribution. Results show that the soil sections with more permeable sediment materials corresponded with higher biomass (total anaerobes > 2 x 106cells/g) and significant contaminant degradation. However, those sections with less permeable sediments contained lower microbial population. Results indicate that the subsurface microorganisms were distributed unevenly in the aquifer, and some regions were devoid of microorganisms and biodegradation activities. Spatial distribution of microorganisms, soil materials, and biogeochemical characteristics in the subsurface soils control the extent and kinetics of contaminant biodegradation. Thus, using blended aquifer materials for measurement of in situ biodegradation rates may not achieve representative results.
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Amo-Seco, M., CG Castro, N. Villacieros-Robineau, F. Alonso-Pérez, R. Graña, G. Rosón, and P. Berg. "Benthic oxygen fluxes in a coastal upwelling system (Ria de Vigo, NW Iberia) measured by aquatic eddy covariance." Marine Ecology Progress Series 670 (July 22, 2021): 15–31. http://dx.doi.org/10.3354/meps13770.
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Organic carbon mineralization and nutrient cycling in benthic environments are critically important for their biogeochemical functioning, but are poorly understood in coastal upwelling systems. The main objective of this study was to determine benthic oxygen fluxes in a muddy sediment in the Ria de Vigo (NW Iberian coastal upwelling), by applying the aquatic eddy covariance (AEC) technique during 2 campaigns in different seasons (June and October 2017). The main drivers of benthic fluxes were studied and compared among days in each season and between seasons. The 2 campaigns were characterized by an upwelling-relaxation period followed by a downwelling event, the last of which was due to the extratropical cyclone Ophelia in October. The mean (±SD) seasonal benthic oxygen fluxes were not significantly different for the 2 campaigns despite differences in hydrodynamic and biogeochemical conditions (June: -20.9 ± 7.1 mmol m-2 d-1 vs. October: -26.5 ± 3.1 mmol m-2 d-1). Benthic fluxes were controlled by different drivers depending on the season. June was characterized by sinking labile organic material, which enhanced benthic fluxes in the downwelling event, whereas October had a significantly higher bottom velocity that stimulated the benthic fluxes. Finally, a comparison with a large benthic chamber (0.50 m2) was made during October. Despite methodological differences between AEC and chamber measurements, concurrent fluxes agreed within an acceptable margin (AEC:benthic chamber ratio = 0.78 ± 0.13; mean ± SD). Bottle incubations of water sampled from the chamber interior indicated that mineralization could explain this difference. These results show the importance of using non-invasive techniques such as AEC to resolve benthic flux dynamics.
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Michalski, Rajmund, Sebastian Szopa, Magdalena Jabłońska, and Aleksandra Łyko. "Application of Hyphenated Techniques in Speciation Analysis of Arsenic, Antimony, and Thallium." Scientific World Journal 2012 (2012): 1–17. http://dx.doi.org/10.1100/2012/902464.
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Due to the fact that metals and metalloids have a strong impact on the environment, the methods of their determination and speciation have received special attention in recent years. Arsenic, antimony, and thallium are important examples of such toxic elements. Their speciation is especially important in the environmental and biomedical fields because of their toxicity, bioavailability, and reactivity. Recently, speciation analytics has been playing a unique role in the studies of biogeochemical cycles of chemical compounds, determination of toxicity and ecotoxicity of selected elements, quality control of food products, control of medicines and pharmaceutical products, technological process control, research on the impact of technological installation on the environment, examination of occupational exposure, and clinical analysis. Conventional methods are usually labor intensive, time consuming, and susceptible to interferences. The hyphenated techniques, in which separation method is coupled with multidimensional detectors, have become useful alternatives. The main advantages of those techniques consist in extremely low detection and quantification limits, insignificant interference, influence as well as high precision and repeatability of the determinations. In view of their importance, the present work overviews and discusses different hyphenated techniques used for arsenic, antimony, and thallium species analysis, in different clinical, environmental and food matrices.
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Borger, Emil De, Justin Tiano, Ulrike Braeckman, Tom Ysebaert, and Karline Soetaert. "Biological and biogeochemical methods for estimating bioirrigation: a case study in the Oosterschelde estuary." Biogeosciences 17, no. 6 (April 1, 2020): 1701–15. http://dx.doi.org/10.5194/bg-17-1701-2020.
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Abstract. Bioirrigation, the exchange of solutes between overlying water and sediment by benthic organisms, plays an important role in sediment biogeochemistry. Bioirrigation either is quantified based on tracer data or a community (bio)irrigation potential (IPc) can be derived based on biological traits. Both these techniques were applied in a seasonal study of bioirrigation in subtidal and intertidal habitats in a temperate estuary. The combination of a tracer time series with a high temporal resolution and a mechanistic model allowed for us to simultaneously estimate the pumping rate and the sediment attenuation, a parameter that determines irrigation depth. We show that, although the total pumping rate is similar in both intertidal and subtidal areas, there is deeper bioirrigation in intertidal areas. This is explained by higher densities of bioirrigators such as Corophium sp., Heteromastus filiformis and Arenicola marina in the intertidal, as opposed to the subtidal, areas. The IPc correlated more strongly with the attenuation coefficient than the pumping rate, which highlights that the IPc index reflects more the bioirrigation depth than the rate.
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Kwiatkowski, L., A. Yool, J. I. Allen, T. R. Anderson, R. Barciela, E. T. Buitenhuis, M. Butenschön, et al. "iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework." Biogeosciences 11, no. 24 (December 19, 2014): 7291–304. http://dx.doi.org/10.5194/bg-11-7291-2014.
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Abstract. Ocean biogeochemistry (OBGC) models span a wide variety of complexities, including highly simplified nutrient-restoring schemes, nutrient–phytoplankton–zooplankton–detritus (NPZD) models that crudely represent the marine biota, models that represent a broader trophic structure by grouping organisms as plankton functional types (PFTs) based on their biogeochemical role (dynamic green ocean models) and ecosystem models that group organisms by ecological function and trait. OBGC models are now integral components of Earth system models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here we present an intercomparison of six OBGC models that were candidates for implementation within the next UK Earth system model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the ocean general circulation model Nucleus for European Modelling of the Ocean (NEMO) and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform all other models across all metrics. Nonetheless, the simpler models are broadly closer to observations across a number of fields and thus offer a high-efficiency option for ESMs that prioritise high-resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low-resolution climate dynamics and high-complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry–climate interactions.
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Thomsen, Soeren, Johannes Karstensen, Rainer Kiko, Gerd Krahmann, Marcus Dengler, and Anja Engel. "Remote and local drivers of oxygen and nitrate variability in the shallow oxygen minimum zone off Mauritania in June 2014." Biogeosciences 16, no. 5 (March 13, 2019): 979–98. http://dx.doi.org/10.5194/bg-16-979-2019.
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Abstract. Upwelling systems play a key role in the global carbon and nitrogen cycles and are also of local relevance due to their high productivity and fish resources. To capture and understand the high spatial and temporal variability in physical and biogeochemical parameters found in these regions, novel measurement techniques have to be combined in an interdisciplinary manner. Here we use high-resolution glider-based physical–biogeochemical observations in combination with ship-based underwater vision profiler, sensor and bottle data to investigate the drivers of oxygen and nitrate variability across the shelf break off Mauritania in June 2014. Distinct oxygen and nitrate variability shows up in our glider data. High-oxygen and low-nitrate anomalies were clearly related to water mass variability and probably linked to ocean transport. Low-oxygen and high-nitrate patches co-occurred with enhanced turbidity signals close to the seabed, which suggests locally high microbial respiration rates of resuspended organic matter near the sea floor. This interpretation is supported by high particle abundance observed by the underwater vision profiler and enhanced particle-based respiration rate estimates close to the seabed. Discrete in situ measurements of dissolved organic carbon and amino acids suggest the formation of dissolved organic carbon due to particle dissolution near the seabed fueling additional microbial respiration. During June an increase in the oxygen concentration on the shelf break of about 15 µmol kg−1 was observed. These changes go along with meridional circulation changes but cannot be explained by typical water mass property changes. Thus our high-resolution interdisciplinary observations highlight the complex interplay of remote and local physical–biogeochemical drivers of oxygen and nitrate variability off Mauritania, which cannot be captured by classical shipboard observations alone.
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Tereshchenko, N. N., S. B. Gulin, and V. Yu Proskurnin. "Radioecological regularities of plutonium alpha-radionuclides redistribution in the Black Sea ecosystem." Marine Biological Journal 1, no. 3 (September 29, 2016): 3–13. http://dx.doi.org/10.21072/mbj.2016.01.3.01.
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The work is devoted to the study of radioecological processes of redistribution of plutonium alpha-radionuclides (239+240Pu) as the main man-maid dose-forming alpha-radionuclides during the period after Chernobyl NPP accident. 239+240Pu are long-lived radioisotopes, the content of which is increasing in natural ecosystems from incident to incident. Radiotoxicity of these radionuclides is high, and we need science-based approaches of assessment and forecast of radioecological condition of the basins being at risk of a radioactive re-contamination, such as the Black Sea as an inland sea located at region close to developed countries using nuclear technologies. The study was performed with modern advanced techniques, the main of them were radiochemical analysis, alpha-spectrometry and radiotracer technologies. As a result of investigation the radiological regularities of plutonium behavior in the Black Sea ecosystem during the post-Chernobyl period were revealed. Quantitative parameters of plutonium migration in the sea were determined: sedimentation rates at different areas of the sea, the 239+240Pu effective half-lives in surface water, the 239+240Pu radiocapacity factor for bottom sediment, the 239+240Pu fluxes, levels of 239+240Pu in the ecosystem components, and the 239+240Pu accumulation factors for biotic and abiotic components. The features of the biogeochemical behavior of plutonium in the Black Sea ecosystem were identified and the conditions and processes causing them were indicated. The increased ability of the Black Sea surface water to self-purification against 239+240Pu, short residence time of plutonium in surface waters, the relatively high rapid of plutonium accumulation in the bottom sediment due to biogeochemical sedimentation of it, the high concentration ability of silt sediment against 239+240Pu and the type of biogeochemical behavior of plutonium in the Black Sea ecosystem has been observed.
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Ribas-Ribas, M., G. L. Cripps, M. Townend, A. J. Poulton, and T. Tyrrell. "Spatial patterns of phytoplankton composition and upper-ocean biogeochemistry do not follow carbonate chemistry gradients in north-west European Shelf seas." ICES Journal of Marine Science 74, no. 4 (May 1, 2017): 965–77. http://dx.doi.org/10.1093/icesjms/fsx063.
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A key difficulty in ocean acidification research is to predict its impact after physiological, phenotypic, and genotypic adaptation has had time to take place. Observational datasets can be a useful tool in addressing this issue. During a cruise in June–July 2011, measurements of upper-ocean biogeochemical variables, climatically active gases and plankton community composition were collected from northwestern European seas. We used various multivariate statistical techniques to assess the relative influences of carbonate chemistry and other environmental factors on these response variables. We found that the spatial patterns in plankton communities were driven more by nutrient availability and physical variables than by carbonate chemistry. The best subset of variables able to account for phytoplankton community structure was the euphotic zone depth, silicic acid availability, mixed layer average irradiance, and nitrate concentration (59% of variance explained). The spatial variations in phytoplankton and coccolithophores species composition were both found to be more strongly associated with nutrients and physical variables than carbonate chemistry, with the latter only explaining 14 and 9% of the variance, respectively. The plankton community composition and contribution of calcifying organisms was not observed to change under lower calcite saturation state (Ω) conditions, although no regions of undersaturation (Ω < 1) were encountered during the cruise. Carbonate chemistry played a more prominent, but still secondary, role in determining dinoflagellate and diatom assemblage composition (20 and 13% of total variance explained, respectively). Nutrient and physical variables also explained more of the spatial variations of most climatically active gases and selected biogeochemical response variables, although some also appeared to be influenced by carbonate chemistry. This observational study has demonstrated that ocean acidification research needs to be set in context with other environmental forcing variables to fully appreciate the primary, or indeed secondary, role that increasing fugacity of carbon dioxide has on biological communities and associated biogeochemical rates.
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Raina, Jean-Baptiste, Dianne Tapiolas, Bette L. Willis, and David G. Bourne. "Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur." Applied and Environmental Microbiology 75, no. 11 (April 3, 2009): 3492–501. http://dx.doi.org/10.1128/aem.02567-08.
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ABSTRACT Marine bacteria play a central role in the degradation of dimethylsulfoniopropionate (DMSP) to dimethyl sulfide (DMS) and acrylic acid, DMS being critical to cloud formation and thereby cooling effects on the climate. High concentrations of DMSP and DMS have been reported in scleractinian coral tissues although, to date, there have been no investigations into the influence of these organic sulfur compounds on coral-associated bacteria. Two coral species, Montipora aequituberculata and Acropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera, Roseobacter, Spongiobacter, Vibrio, and Alteromonas, which were isolated on media with either DMSP or DMS as the sole carbon source, comprised the majority of clones retrieved from coral mucus and tissue 16S rRNA gene clone libraries. Clones affiliated with Roseobacter sp. constituted 28% of the M. aequituberculata tissue libraries, while 59% of the clones from the A. millepora libraries were affiliated with sequences related to the Spongiobacter genus. Vibrio spp. were commonly isolated from DMS and acrylic acid enrichments and were also present in 16S rRNA gene libraries from coral mucus, suggesting that under “normal” environmental conditions, they are a natural component of coral-associated communities. Genes homologous to dddD, and dddL, previously implicated in DMSP degradation, were also characterized from isolated strains, confirming that bacteria associated with corals have the potential to metabolize this sulfur compound when present in coral tissues. Our results demonstrate that DMSP, DMS, and acrylic acid potentially act as nutrient sources for coral-associated bacteria and that these sulfur compounds are likely to play a role in structuring bacterial communities in corals, with important consequences for the health of both corals and coral reef ecosystems.
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Garayburu-Caruso, Vanessa A., Robert E. Danczak, James C. Stegen, Lupita Renteria, Marcy Mccall, Amy E. Goldman, Rosalie K. Chu, et al. "Using Community Science to Reveal the Global Chemogeography of River Metabolomes." Metabolites 10, no. 12 (December 20, 2020): 518. http://dx.doi.org/10.3390/metabo10120518.
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River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water and sediment metabolomes using ultrahigh-resolution techniques. Here, we describe a community science effort from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to characterize global metabolomes in surface water and sediment that span multiple stream orders and biomes. We describe the distribution of key aspects of metabolomes including elemental groups, chemical classes, indices, and inferred biochemical transformations. We show that metabolomes significantly differ across surface water and sediment and that surface water metabolomes are more rich and variable. We also use inferred biochemical transformations to identify core metabolic processes shared among surface water and sediment. Finally, we observe significant spatial variation in sediment metabolites between rivers in the eastern and western portions of the contiguous United States. Our work not only provides a basis for understanding global patterns in river corridor biogeochemical cycles but also demonstrates that community science endeavors can enable global research projects that are unfeasible with traditional research models.
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de Montera, L., M. Jouini, S. Verrier, S. Thiria, and M. Crepon. "Multifractal analysis of oceanic chlorophyll maps remotely sensed from space." Ocean Science Discussions 8, no. 1 (January 21, 2011): 55–84. http://dx.doi.org/10.5194/osd-8-55-2011.
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Abstract. Phytoplankton patchiness has been investigated with multifractal analysis techniques. We analyzed oceanic chlorophyll maps, measured by the SeaWiFS orbiting sensor, which are considered to be good proxies for phytoplankton. Multifractal properties are observed, from the sub-mesoscale up to the mesoscale, and are found to be consistent with the Corssin-Obukhov scale law of passive scalars. This result indicates that, within this scale range, turbulent mixing would be the dominant effect leading to the observed variability of phytoplankton fields. Finally, it is shown that multifractal patchiness can be responsible for significant biases in the nonlinear source and sink terms involved in biogeochemical numerical models.
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Smith, Katherine M., Skyler Kern, Peter E. Hamlington, Marco Zavatarelli, Nadia Pinardi, Emily F. Klee, and Kyle E. Niemeyer. "BFM17 v1.0: a reduced biogeochemical flux model for upper-ocean biophysical simulations." Geoscientific Model Development 14, no. 5 (May 5, 2021): 2419–42. http://dx.doi.org/10.5194/gmd-14-2419-2021.
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Abstract. We present a newly developed upper-thermocline, open-ocean biogeochemical flux model that is complex and flexible enough to capture open-ocean ecosystem dynamics but reduced enough to incorporate into highly resolved numerical simulations and parameter optimization studies with limited additional computational cost. The model, which is derived from the full 56-state-variable Biogeochemical Flux Model (BFM56; Vichi et al., 2007), follows a biological and chemical functional group approach and allows for the development of critical non-Redfield nutrient ratios. Matter is expressed in units of carbon, nitrogen, and phosphate, following techniques used in more complex models. To reduce the overall computational cost and to focus on upper-thermocline, open-ocean, and non-iron-limited or non-silicate-limited conditions, the reduced model eliminates certain processes, such as benthic, silicate, and iron influences, and parameterizes others, such as the bacterial loop. The model explicitly tracks 17 state variables, divided into phytoplankton, zooplankton, dissolved organic matter, particulate organic matter, and nutrient groups. It is correspondingly called the Biogeochemical Flux Model 17 (BFM17). After describing BFM17, we couple it with the one-dimensional Princeton Ocean Model for validation using observational data from the Sargasso Sea. The results agree closely with observational data, giving correlations above 0.85, except for chlorophyll (0.63) and oxygen (0.37), as well as with corresponding results from BFM56, with correlations above 0.85, except for oxygen (0.56), including the ability to capture the subsurface chlorophyll maximum and bloom intensity. In comparison to previous models of similar size, BFM17 provides improved correlations between several model output fields and observational data, indicating that reproduction of in situ data can be achieved with a low number of variables, while maintaining the functional group approach. Notable additions to BFM17 over similar complexity models are the explicit tracking of dissolved oxygen, allowance for non-Redfield nutrient ratios, and both dissolved and particulate organic matter, all within the functional group framework.
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Pieńkowski, Anna J., Navpreet K. Gill, Mark FA Furze, Samuel M. Mugo, Fabienne Marret, and Abbey Perreaux. "Arctic sea-ice proxies: Comparisons between biogeochemical and micropalaeontological reconstructions in a sediment archive from Arctic Canada." Holocene 27, no. 5 (November 29, 2016): 665–82. http://dx.doi.org/10.1177/0959683616670466.
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Boxcore 99LSSL-001 from the southwest Canadian Arctic Archipelago (68.095°N, 114.186°W), studied by multiproxy approaches (sea-ice diatom biomarker IP25, phytoplankton-based biomarker brassicasterol, biogenic silica, total organic carbon, dinoflagellate cysts = dinocysts, diatoms) and their applications (sea-ice index PBIP25, modern analogue technique (MAT) transfer functions), provides a chronologically constrained (210Pb, 137Cs, two 14C dates) palaeoenvironmental archive spanning AD 1625–1999 with which to compare and evaluate proxies frequently used in sea-ice reconstructions. Whereas diatoms are rare, PBIP25, biogenic silica and qualitative dinocyst approaches show good agreement, suggesting that palaeo sea-ice histories based on biomarker and microfossil techniques are robust in this region. These combined approaches show fluctuating long open water to marginal ice zone conditions (AD 1625–1740), followed by high-amplitude oscillations between long open water and extended spring/summer sea ice (AD 1740–1870). Greater ice cover (AD 1870–1970) precedes recent reductions in seasonal sea ice (AD 1970–1999). Dinocyst-based MAT, however, produces a low-amplitude signal lacking the nuances of other proxies, with most probable sea-ice reconstructions poorly correlating with biomarker-based histories. Explanations for this disagreement may include limited spatial coverage in the modern dinocyst distribution database for MAT and the broad environmental tolerances of polar dinocysts. Overall, PBIP25 provides the most detailed palaeo sea-ice signal, although its use in a shallow polar archipelago downcore setting poses methodological challenges. This proxy comparison demonstrates the limitations of palaeo sea-ice reconstructions and emphasizes the need for calibration studies tying modern microfossil and biogeochemical proxies to directly measured oceanographic parameters, as a springboard for robust quantitative palaeo studies.
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Hague, Mark, and Marcello Vichi. "Southern Ocean Biogeochemical Argo detect under-ice phytoplankton growth before sea ice retreat." Biogeosciences 18, no. 1 (January 4, 2021): 25–38. http://dx.doi.org/10.5194/bg-18-25-2021.
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Abstract. The seasonality of sea ice in the Southern Ocean has profound effects on the life cycle (phenology) of phytoplankton residing under the ice. The current literature investigating this relationship is primarily based on remote sensing, which often lacks data for half of the year or more. One prominent hypothesis holds that, following ice retreat in spring, buoyant meltwaters enhance available irradiance, triggering a bloom which follows the ice edge. However, an analysis of Biogeochemical Argo (BGC-Argo) data sampling under Antarctic sea ice suggests that this is not necessarily the case. Rather than precipitating rapid accumulation, we show that meltwaters enhance growth in an already highly active phytoplankton population. Blooms observed in the wake of the receding ice edge can then be understood as the emergence of a growth process that started earlier under sea ice. Indeed, we estimate that growth initiation occurs, on average, 4–5 weeks before ice retreat, typically starting in August and September. Novel techniques using on-board data to detect the timing of ice melt were used. Furthermore, such growth is shown to occur under conditions of substantial ice cover (>90 % satellite ice concentration) and deep mixed layers (>100 m), conditions previously thought to be inimical to growth. This led to the development of several box model experiments (with varying vertical depth) in which we sought to investigate the mechanisms responsible for such early growth. The results of these experiments suggest that a combination of higher light transfer (penetration) through sea ice cover and extreme low light adaptation by phytoplankton can account for the observed phenology.
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Shuster, Jeremiah, Maria Rea, Barbara Etschmann, Joël Brugger, and Frank Reith. "Terraced Iron Formations: Biogeochemical Processes Contributing to Microbial Biomineralization and Microfossil Preservation." Geosciences 8, no. 12 (December 13, 2018): 480. http://dx.doi.org/10.3390/geosciences8120480.
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Terraced iron formations (TIFs) are laminated structures that cover square meter-size areas on the surface of weathered bench faces and tailings piles at the Mount Morgan mine, which is a non-operational open pit mine located in Queensland, Australia. Sampled TIFs were analyzed using molecular and microanalytical techniques to assess the bacterial communities that likely contributed to the development of these structures. The bacterial community from the TIFs was more diverse compared to the tailings on which the TIFs had formed. The detection of both chemolithotrophic iron-oxidizing bacteria, i.e., Acidithiobacillus ferrooxidans and Mariprofundus ferrooxydans, and iron-reducing bacteria, i.e., Acidobacterium capsulatum, suggests that iron oxidation/reduction are continuous processes occurring within the TIFs. Acidophilic, iron-oxidizing bacteria were enriched from the TIFs. High-resolution electron microscopy was used to characterize iron biomineralization, i.e., the association of cells with iron oxyhydroxide mineral precipitates, which served as an analog for identifying the structural microfossils of individual cells as well as biofilms within iron oxyhydroxide laminations—i.e., alternating layers containing schwertmannite (Fe16O16(OH)12(SO4)2) and goethite (FeO(OH)). Kinetic modeling estimated that it would take between 0.25–2.28 years to form approximately one gram of schwertmannite as a lamination over a one-m2 surface, thereby contributing to TIF development. This length of time could correspond with seasonable rainfall or greater than average annual rainfall. In either case, the presence of water is critical for sustaining microbial activity, and subsequently iron oxyhydroxide mineral precipitation. The TIFs from the Mount Morgan mine also contain laminations of gypsum (CaSO·2H2O) alternating with iron oxyhydroxide laminations. These gypsum laminations likely represented drier periods of the year, in which millimeter-size gypsum crystals presumably precipitated as water gradually evaporated. Interestingly, gypsum acted as a substrate for the attachment of cells and the growth of biofilms that eventually became mineralized within schwertmannite and goethite. The dissolution and reprecipitation of gypsum suggest that microenvironments with circumneutral pH conditions could exist within TIFs, thereby supporting iron oxidation under circumneutral pH conditions. In conclusion, this study highlights the relationship between microbes for the development of TIFs and also provides interpretations of biogeochemical processes contributing to the preservation of bacterial cells and entire biofilms under acidic conditions.
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Gačić, Miroslav, and Manuel Bensi. "Ocean Exchange and Circulation." Water 12, no. 3 (March 20, 2020): 882. http://dx.doi.org/10.3390/w12030882.
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The great spatial and temporal variability, which characterizes the marine environment, requires a huge effort to be observed and studied properly since changes in circulation and mixing processes directly influence the variability of the physical and biogeochemical properties. A multi-platform approach and a collaborative effort, in addition to optimizing both data collection and quality, is needed to bring the scientific community to more efficient monitoring and predicting of the world ocean processes. This Special Issue consists of nine original scientific articles that address oceanic circulation and water mass exchange. Most of them deal with mean circulation, basin and sub-basin-scale flows, mesoscale eddies, and internal processes (e.g., mixing and internal waves) that contribute to the redistribution of oceanic properties and energy within the ocean. One paper deals with numerical modelling application finalized to evaluate the capacity of coastal vegetated areas to mitigate the impact of a tsunami. The study areas in which these topics are developed include both oceanic areas and semi-enclosed seas such as the Mediterranean Sea, the Norwegian Sea and the Fram Strait, the South China Sea, and the Northwest Pacific. Scientific findings presented in this Special Issue highlight how a combination of various modern observation techniques can improve our understanding of the complex physical and biogeochemical processes in the ocean.
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Sato, M., R. Sakuraba, and F. Hashihama. "Phosphate monoesterase and diesterase activities in the North and South Pacific Ocean." Biogeosciences Discussions 10, no. 6 (June 20, 2013): 10095–124. http://dx.doi.org/10.5194/bgd-10-10095-2013.
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Abstract. To reveal the biogeochemical cycling of phosphorus in the Pacific Ocean, phosphate monoesterase and diesterase activities were measured with soluble reactive phosphorus (SRP) and labile and total dissolved organic phosphorus (DOP) concentrations in the North and South Pacific Ocean. Both esterase activities were noticeably enhanced around the western part of 30° N, where the surface SRP concentration was below 10 nM, while they showed no significant correlation with DOP concentration. The proportion of the activity in the dissolved fraction was higher for diesterase than monoesterase, which may support results from previous genomic analyses. Substrate affinity and the maximum hydrolysis rate of monoesterase were the highest at lower concentrations of SRP, showing the adaptation of microbes to inorganic phosphorus nutrient deficiency at the molecular level. The calculated turnover time of monoesters was 1 to 2 weeks in the western North Pacific Ocean, which was much shorter than the turnover time in other areas of the Pacific Ocean but longer than the turnover time in other phosphate-depleted areas. In contrast, the turnover rate of diesters was calculated to exceed 100 days, revealing that diesters in the western North Pacific were a biologically refractory phosphorus fraction. In future studies, a combination of molecular biological techniques and kinetic studies will reveal the entire process of biogeochemical cycling of phosphorus in the ocean, including components that were not elucidated in the present study.
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Fytianos, Konstantinos. "Speciation Analysis of Heavy Metals in Natural Waters: A Review." Journal of AOAC INTERNATIONAL 84, no. 6 (November 1, 2001): 1763–69. http://dx.doi.org/10.1093/jaoac/84.6.1763.
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Abstract Metal speciation in natural waters is of increasing interest and importance because toxicity, bioavailability, environmental mobility, biogeochemical behavior, and potential risk in general are strongly dependent on the chemical species of metals. This paper provides an overview of the need for speciation of heavy metals in natural waters, the chemical and toxicological aspects of speciation, and the analytical procedures for separation and the different techniques for final determination that are used today. The trends and developments of speciation are also discussed. Finally, the case of chromium (Cr) was selected for a detailed presentation because the speciation of this metal has attracted a great deal of interest in view of the toxic properties of Cr(VI).
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Kwiatkowski, L., A. Yool, J. I. Allen, T. R. Anderson, R. Barciela, E. T. Buitenhuis, M. Butenschön, et al. "iMarNet: an ocean biogeochemistry model inter-comparison project within a common physical ocean modelling framework." Biogeosciences Discussions 11, no. 7 (July 10, 2014): 10537–69. http://dx.doi.org/10.5194/bgd-11-10537-2014.
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Abstract. Ocean biogeochemistry (OBGC) models span a wide range of complexities from highly simplified, nutrient-restoring schemes, through nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, through to models that represent a broader trophic structure by grouping organisms as plankton functional types (PFT) based on their biogeochemical role (Dynamic Green Ocean Models; DGOM) and ecosystem models which group organisms by ecological function and trait. OBGC models are now integral components of Earth System Models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here, we present an inter-comparison of six OBGC models that were candidates for implementation within the next UK Earth System Model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the Nucleus for the European Modelling of the Ocean (NEMO) ocean general circulation model (GCM), and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform or underperform all other models across all metrics. Nonetheless, the simpler models that are easier to tune are broadly closer to observations across a number of fields, and thus offer a high-efficiency option for ESMs that prioritise high resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low resolution climate dynamics and high complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry–climate interactions.