WorldWideScience

Sample records for modeling marine microbial

  1. A model for microbial phosphorus cycling in bioturbated marine sediments

    DEFF Research Database (Denmark)

    Dale, Andrew W.; Boyle, R. A.; Lenton, Timothy M.

    2016-01-01

    A diagenetic model is used to simulate the diagenesis and burial of particulate organic carbon (Corg) and phosphorus (P) in marine sediments underlying anoxic versus oxic bottom waters. The latter are physically mixed by animals moving through the surface sediment (bioturbation) and ventilated...... P pump) allows preferential mineralization of the bulk Porg pool relative to Corg during both aerobic and anaerobic respiration and is consistent with the database. Results with this model show that P burial is strongly enhanced in sediments hosting fauna. Animals mix highly labile Porg away from....... The results also help to explain Corg:Porg ratios in the geological record and the persistence of Porg in ancient marine sediments. © 2016 Elsevier Ltd....

  2. MATHEMATICAL MODELING OF THE ELECTRIC CURRENT GENERATION IN A MICROBIAL FUEL CELL INOCULATED WITH MARINE SEDIMENT

    Directory of Open Access Journals (Sweden)

    J. T. Teleken

    Full Text Available Abstract Microbial fuel cells (MFC are electrochemical devices that utilize the ability of some microorganisms to oxidize organic matter and transfer electrons resulting from their metabolism to an insoluble acceptor. The goal of the present study was to model the kinetics of electrical current generation from an MFC inoculated with marine sediment. For this purpose, a differential equation system was used, including the Nernst-Monod relationship and Ohm's Law, to describe the microbial metabolism and the mechanism of extracellular electron transfer (EET, respectively. The experimental data obtained by cyclic voltammetry analysis were properly described by the model. It was concluded that marine microorganisms preferably use a direct mechanism of EET by means of nanowires to establish the electrochemical contact with the anode. The mathematical modeling could help understand MFC operation and, consequently, contribute to improving power generation from this source.

  3. Satellite remote sensing data can be used to model marine microbial metabolite turnover

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, Peter E.; Scott, Nicole; Post, Anton F.; Field, Dawn; Knight, Rob; Hamada, Yuki; Gilbert, Jack A.

    2014-07-29

    Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10-6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.

  4. Marine sponges as microbial fermenters

    OpenAIRE

    Hentschel, Ute; Usher, Kayley M.; Taylor, Michael W.

    2006-01-01

    The discovery of phylogenetically complex, yet highly sponge-specific microbial communities in marine sponges, including novel lineages and even candidate phyla, came as a surprise. At the same time, unique research opportunities opened up, because the microorganisms of sponges are in many ways more accessible than those of seawater. Accordingly, we consider sponges as microbial fermenters that provide exciting new avenues in marine microbiology and biotechnology. This review covers recent fi...

  5. Marine sponges as microbial fermenters.

    Science.gov (United States)

    Hentschel, Ute; Usher, Kayley M; Taylor, Michael W

    2006-02-01

    The discovery of phylogenetically complex, yet highly sponge-specific microbial communities in marine sponges, including novel lineages and even candidate phyla, came as a surprise. At the same time, unique research opportunities opened up, because the microorganisms of sponges are in many ways more accessible than those of seawater. Accordingly, we consider sponges as microbial fermenters that provide exciting new avenues in marine microbiology and biotechnology. This review covers recent findings regarding diversity, biogeography and population dynamics of sponge-associated microbiota, and the data are discussed within the larger context of the microbiology of the ocean.

  6. Microbial quality of a marine tidal pool

    CSIR Research Space (South Africa)

    Genthe, Bettina

    1995-01-01

    Full Text Available In this study the source of microbial pollution to a tidal pool was investigated. Both adjacent seawater which could contribute to possible faecal pollution and potential direct bather pollution were studied. The microbial quality of the marine...

  7. Anthropogenic perturbations in marine microbial communities.

    Science.gov (United States)

    Nogales, Balbina; Lanfranconi, Mariana P; Piña-Villalonga, Juana M; Bosch, Rafael

    2011-03-01

    Human activities impact marine ecosystems at a global scale and all levels of complexity of life. Despite their importance as key players in ecosystem processes, the stress caused to microorganisms has been greatly neglected. This fact is aggravated by difficulties in the analysis of microbial communities and their high diversity, making the definition of patterns difficult. In this review, we discuss the effects of nutrient increase, pollution by organic chemicals and heavy metals and the introduction of antibiotics and pathogens into the environment. Microbial communities respond positively to nutrients and chemical pollution by increasing cell numbers. There are also significant changes in community composition, increases in diversity and high temporal variability. These changes, which evidence the modification of the environmental conditions due to anthropogenic stress, usually alter community functionality, although this aspect has not been explored in depth. Altered microbial communities in human-impacted marine environments can in turn have detrimental effects on human health (i.e. spread of pathogens and antibiotic resistance). New threats to marine ecosystems, i.e. related to climate change, could also have an impact on microbial communities. Therefore, an effort dedicated to analyse the microbial compartment in detail should be made when studying the impact of anthropogenic activities on marine ecosystems. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  8. Development of a predictive model for the growth kinetics of aerobic microbial population on pomegranate marinated chicken breast fillets under isothermal and dynamic temperature conditions.

    Science.gov (United States)

    Lytou, Anastasia; Panagou, Efstathios Z; Nychas, George-John E

    2016-05-01

    The aim of this study was the development of a model to describe the growth kinetics of aerobic microbial population of chicken breast fillets marinated in pomegranate juice under isothermal and dynamic temperature conditions. Moreover, the effect of pomegranate juice on the extension of the shelf life of the product was investigated. Samples (10 g) of chicken breast fillets were immersed in marinades containing pomegranate juice for 3 h at 4 °C following storage under aerobic conditions at 4, 10, and 15 °C for 10 days. Total Viable Counts (TVC), Pseudomonas spp and lactic acid bacteria (LAB) were enumerated, in parallel with sensory assessment (odor and overall appearance) of marinated and non-marinated samples. The Baranyi model was fitted to the growth data of TVC to calculate the maximum specific growth rate (μmax) that was further modeled as a function of temperature using a square root-type model. The validation of the model was conducted under dynamic temperature conditions based on two fluctuating temperature scenarios with periodic changes from 6 to 13 °C. The shelf life was determined both mathematically and with sensory assessment and its temperature dependence was modeled by an Arrhenius type equation. Results showed that the μmax of TVC of marinated samples was significantly lower compared to control samples regardless temperature, while under dynamic temperature conditions the model satisfactorily predicted the growth of TVC in both control and marinated samples. The shelf-life of marinated samples was significantly extended compared to the control (5 days extension at 4 °C). The calculated activation energies (Ea), 82 and 52 kJ/mol for control and marinated samples, respectively, indicated higher temperature dependence of the shelf life of control samples compared to marinated ones. The present results indicated that pomegranate juice could be used as an alternative ingredient in marinades to prolong the shelf life of chicken. Copyright © 2015

  9. Marine snow microbial communities: scaling of abundances with aggregate size

    DEFF Research Database (Denmark)

    Kiørboe, Thomas

    2003-01-01

    Marine aggregates are inhabited by diverse microbial communities, and the concentration of attached microbes typically exceeds concentrations in the ambient water by orders of magnitude. An extension of the classical Lotka-Volterra model, which includes 3 trophic levels (bacteria, flagellates...... are controlled by flagellate grazing, while flagellate and ciliate populations are governed by colonization and detachment. The model also suggests that microbial populations are turned over rapidly (1 to 20 times d-1) due to continued colonization and detachment. The model overpredicts somewhat the scaling...... of microbial abundances with aggregate size observed in field-collected aggregates. This may be because it disregards the aggregation/disaggregation dynamics of aggregates, as well as interspecific interactions between bacteria....

  10. Research and Application of Marine Microbial Enzymes: Status and Prospects

    Science.gov (United States)

    Zhang, Chen; Kim, Se-Kwon

    2010-01-01

    Over billions of years, the ocean has been regarded as the origin of life on Earth. The ocean includes the largest range of habitats, hosting the most life-forms. Competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. The evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. Therefore, marine microbial enzymes can offer novel biocatalysts with extraordinary properties. This review deals with the research and development work investigating the occurrence and bioprocessing of marine microbial enzymes. PMID:20631875

  11. Research and Application of Marine Microbial Enzymes: Status and Prospects

    Directory of Open Access Journals (Sweden)

    Chen Zhang

    2010-06-01

    Full Text Available Over billions of years, the ocean has been regarded as the origin of life on Earth. The ocean includes the largest range of habitats, hosting the most life-forms. Competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. The evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. Therefore, marine microbial enzymes can offer novel biocatalysts with extraordinary properties. This review deals with the research and development work investigating the occurrence and bioprocessing of marine microbial enzymes.

  12. Research and application of marine microbial enzymes: status and prospects.

    Science.gov (United States)

    Zhang, Chen; Kim, Se-Kwon

    2010-06-23

    Over billions of years, the ocean has been regarded as the origin of life on Earth. The ocean includes the largest range of habitats, hosting the most life-forms. Competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. The evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. Therefore, marine microbial enzymes can offer novel biocatalysts with extraordinary properties. This review deals with the research and development work investigating the occurrence and bioprocessing of marine microbial enzymes.

  13. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

    DEFF Research Database (Denmark)

    Weitz, Joshua S.; Stock, Charles A.; Wilhelm, Steven W.

    2015-01-01

    that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.The ISME Journal...

  14. Marine microbial ecology in a molecular world: what does the future hold?

    Directory of Open Access Journals (Sweden)

    David A. Caron

    2005-06-01

    Full Text Available Advances in genetic and immunological approaches during the last few decades have transformed medicine and biomedical research. The human genome and the genomes of numerous model organisms are now fully sequenced. Initial exploitation of this wealth of genetic information has begun to revolutionize research on these species, and the applications derived from it. Progress in understanding the ecology of microorganisms (including marine taxa has followed closely on the heels of these advances, owing to the tremendous benefit afforded by major technological advances in biomedicine. Through the application of these novel approaches and new technologies, marine microbial ecology has moved from a minor footnote within marine biology and biological oceanography during the 1950s and ‘60s to the focus of much of our present interest in the ocean. During the intervening half-century we have learned a great deal regarding the overall abundances, distributions and activities of microorganisms in the sea. Recognition of the extraordinary diversity of marine microbes, the predominant role that they play in global biogeochemical processes, and the potential for natural or engineered microbial products to benefit humankind, has placed marine microbes in the spotlight of both scientific and popular attention. Our fascination with these minute denizens of the ocean is not likely to wane anytime soon. Recent studies have indicated that we still know relatively little about the breadth of microbial diversity in marine ecosystems. In addition, many (most? of the predominant marine microbial forms in nature have not yet been brought into laboratory culture. Thus, our knowledge is still rudimentary with respect to the spectra of biochemical, physiological and behavioral abilities of these species, and the study of marine microbes will remain a major focus of investigations in marine science well into the foreseeable future. As a large cadre of researchers moves

  15. Microbial Surface Colonization and Biofilm Development in Marine Environments.

    Science.gov (United States)

    Dang, Hongyue; Lovell, Charles R

    2016-03-01

    Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. Marine and estuarine natural microbial biofilms: ecological and biogeochemical dimensions

    Directory of Open Access Journals (Sweden)

    O. Roger Anderson

    2016-08-01

    Full Text Available Marine and estuarine microbial biofilms are ubiquitously distributed worldwide and are increasingly of interest in basic and applied sciences because of their unique structural and functional features that make them remarkably different from the biota in the plankton. This is a review of some current scientific knowledge of naturally occurring microbial marine and estuarine biofilms including prokaryotic and microeukaryotic biota, but excluding research specifically on engineering and applied aspects of biofilms such as biofouling. Because the microbial communities including bacteria and protists are integral to the fundamental ecological and biogeochemical processes that support biofilm communities, particular attention is given to the structural and ecological aspects of microbial biofilm formation, succession, and maturation, as well as the dynamics of the interactions of the microbiota in biofilms. The intent is to highlight current state of scientific knowledge and possible avenues of future productive research, especially focusing on the ecological and biogeochemical dimensions.

  17. Immense Essence of Excellence: Marine Microbial Bioactive Compounds

    Directory of Open Access Journals (Sweden)

    Ira Bhatnagar

    2010-10-01

    Full Text Available Oceans have borne most of the biological activities on our planet. A number of biologically active compounds with varying degrees of action, such as anti-tumor, anti-cancer, anti-microtubule, anti-proliferative, cytotoxic, photo protective, as well as antibiotic and antifouling properties, have been isolated to date from marine sources. The marine environment also represents a largely unexplored source for isolation of new microbes (bacteria, fungi, actinomycetes, microalgae-cyanobacteria and diatoms that are potent producers of bioactive secondary metabolites. Extensive research has been done to unveil the bioactive potential of marine microbes (free living and symbiotic and the results are amazingly diverse and productive. Some of these bioactive secondary metabolites of microbial origin with strong antibacterial and antifungal activities are being intensely used as antibiotics and may be effective against infectious diseases such as HIV, conditions of multiple bacterial infections (penicillin, cephalosporines, streptomycin, and vancomycin or neuropsychiatric sequelae. Research is also being conducted on the general aspects of biophysical and biochemical properties, chemical structures and biotechnological applications of the bioactive substances derived from marine microorganisms, and their potential use as cosmeceuticals and nutraceuticals. This review is an attempt to consolidate the latest studies and critical research in this field, and to showcase the immense competence of marine microbial flora as bioactive metabolite producers. In addition, the present review addresses some effective and novel approaches of procuring marine microbial compounds utilizing the latest screening strategies of drug discovery.

  18. Tropical marine ecosystems: The microbial component

    Digital Repository Service at National Institute of Oceanography (India)

    Chandramohan, D.

    Microbes such as bacteria, fungi and unicellular algae assume greater importance in the tropical marine ecosystems because of their abundance, biomass and activity in a number of chemical and biological processes that provide the driving force...

  19. Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

    Directory of Open Access Journals (Sweden)

    Alan D. W. Dobson

    2010-03-01

    Full Text Available The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.

  20. REVIEW PAPER-MARINE MICROBIAL BIOACTIVE COMPOUNDS

    OpenAIRE

    Kalyani. P*, Hemalatha. K. P. J

    2016-01-01

    Oceans have borne most of the biological activities on our planet. A number of biologically active compounds with varying degrees of action, such as anti-tumor, anti-cancer, anti-microtubule, anti-proliferative, cytotoxic, photo protective, as well as antibiotic and antifouling properties, have been isolated to date from marine sources. The marine environment also represents a largely unexplored source for isolation of new microbes (bacteria, fungi, actinomycetes, microalgae-cyanobacteria and...

  1. Effects of marine microbial biofilms on the biocide release rate from antifouling paints – A model-based analysis

    DEFF Research Database (Denmark)

    Yebra, Diego Meseguer; Kiil, Søren; Erik Weinell, Claus

    2006-01-01

    The antifouling (AF) paint model of Kiil et al. [S. Kiil, C.E. Weinell, M.S. Pedersen, K. Dam-Johansen, Analysis of self-polishing antifouling paints using rotary experiments and mathematical modelling, Ind. Eng. Chem. Res. 40 (2001) 3906-3920] and the simplified biofilm. growth model of Gujer......, polishing behaviour of AF paints. It is concluded that the perturbation of the local sea water conditions (e.g. pH), as a consequence of the metabolic activity of the biofilm should not affect the net biocide leaching and binder reaction rates significantly. This results from the thin and poorly active...... biofilms which presumably grow onto the highly effective modern AF paints. According to simulations, the experimental decrease in the biocide leaching rate caused by biofilm growth must be mainly attributed to adsorption of the biocide by the exopolymeric substances secreted by the microorganisms...

  2. Quorum Sensing in Marine Microbial Environments

    Science.gov (United States)

    Hmelo, Laura R.

    2017-01-01

    Quorum sensing (QS) is a form of chemical communication used by certain bacteria that regulates a wide range of biogeochemically important bacterial behaviors. Although QS was first observed in a marine bacterium nearly four decades ago, only in the past decade has there been a rise in interest in the role that QS plays in the ocean. It has become clear that QS, regulated by signals such as acylated homoserine lactones (AHLs) or furanosyl-borate diesters [autoinducer-2 (AI-2) molecules], is involved in important processes within the marine carbon cycle, in the health of coral reef ecosystems, and in trophic interactions between a range of eukaryotes and their bacterial associates. The most well-studied QS systems in the ocean occur in surface-attached (biofilm) communities and rely on AHL signaling. AHL-QS is highly sensitive to the chemical and biological makeup of the environment and may respond to anthropogenic change, including ocean acidification and rising sea surface temperatures.

  3. Microbial diversity and stratification of South Pacific abyssal marine sediments.

    Science.gov (United States)

    Durbin, Alan M; Teske, Andreas

    2011-12-01

    Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  4. Chemoattraction to dimethylsulfoniopropionate throughout the marine microbial food web.

    Science.gov (United States)

    Seymour, Justin R; Simó, Rafel; Ahmed, Tanvir; Stocker, Roman

    2010-07-16

    Phytoplankton-produced dimethylsulfoniopropionate (DMSP) provides underwater and atmospheric foraging cues for several species of marine invertebrates, fish, birds, and mammals. However, its role in the chemical ecology of marine planktonic microbes is largely unknown, and there is evidence for contradictory functions. By using microfluidics and image analysis of swimming behavior, we observed attraction toward microscale pulses of DMSP and related compounds among several motile strains of phytoplankton, heterotrophic bacteria, and bacterivore and herbivore microzooplankton. Because microbial DMSP cycling is the main natural source of cloud-forming sulfur aerosols, our results highlight how adaptations to microscale chemical seascapes shape planktonic food webs, while potentially influencing climate at the global scale.

  5. A Marine Traffic Flow Model

    Directory of Open Access Journals (Sweden)

    Tsz Leung Yip

    2013-03-01

    Full Text Available A model is developed for studying marine traffic flow through classical traffic flow theories, which can provide us with a better understanding of the phenomenon of traffic flow of ships. On one hand, marine traffic has its special features and is fundamentally different from highway, air and pedestrian traffic. The existing traffic models cannot be simply extended to marine traffic without addressing marine traffic features. On the other hand, existing literature on marine traffic focuses on one ship or two ships but does not address the issues in marine traffic flow.

  6. Microbial activity in the marine deep biosphere: progress and prospects.

    Science.gov (United States)

    Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

    2013-01-01

    The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

  7. Modeling microbial growth and dynamics.

    Science.gov (United States)

    Esser, Daniel S; Leveau, Johan H J; Meyer, Katrin M

    2015-11-01

    Modeling has become an important tool for widening our understanding of microbial growth in the context of applied microbiology and related to such processes as safe food production, wastewater treatment, bioremediation, or microbe-mediated mining. Various modeling techniques, such as primary, secondary and tertiary mathematical models, phenomenological models, mechanistic or kinetic models, reactive transport models, Bayesian network models, artificial neural networks, as well as agent-, individual-, and particle-based models have been applied to model microbial growth and activity in many applied fields. In this mini-review, we summarize the basic concepts of these models using examples and applications from food safety and wastewater treatment systems. We further review recent developments in other applied fields focusing on models that explicitly include spatial relationships. Using these examples, we point out the conceptual similarities across fields of application and encourage the combined use of different modeling techniques in hybrid models as well as their cross-disciplinary exchange. For instance, pattern-oriented modeling has its origin in ecology but may be employed to parameterize microbial growth models when experimental data are scarce. Models could also be used as virtual laboratories to optimize experimental design analogous to the virtual ecologist approach. Future microbial growth models will likely become more complex to benefit from the rich toolbox that is now available to microbial growth modelers.

  8. Microbial community structure affects marine dissolved organic matter composition

    Directory of Open Access Journals (Sweden)

    Elizabeth B Kujawinski

    2016-04-01

    Full Text Available Marine microbes are critical players in the global carbon cycle, affecting both the reduction of inorganic carbon and the remineralization of reduced organic compounds back to carbon dioxide. Members of microbial consortia all depend on marine dissolved organic matter (DOM and in turn, affect the molecules present in this heterogeneous pool. Our understanding of DOM produced by marine microbes is biased towards single species laboratory cultures or simplified field incubations, which exclude large phototrophs and protozoan grazers. Here we explore the interdependence of DOM composition and bacterial diversity in two mixed microbial consortia from coastal seawater: a whole water community and a <1.0-μm community dominated by heterotrophic bacteria. Each consortium was incubated with isotopically-labeled glucose for 9 days. Using stable-isotope probing techniques and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry, we show that the presence of organisms larger than 1.0-μm is the dominant factor affecting bacterial diversity and low-molecular-weight (<1000 Da DOM composition over this experiment. In the <1.0-μm community, DOM composition was dominated by compounds with lipid and peptide character at all time points, confirmed by fragmentation spectra with peptide-containing neutral losses. In contrast, DOM composition in the whole water community was nearly identical to that in the initial coastal seawater. These differences in DOM composition persisted throughout the experiment despite shifts in bacterial diversity, underscoring an unappreciated role for larger microorganisms in constraining DOM composition in the marine environment.

  9. Advances in Marine Microbial Symbionts in the China Sea and Related Pharmaceutical Metabolites

    Directory of Open Access Journals (Sweden)

    Zhiyong Li

    2009-04-01

    Full Text Available Marine animals and plants such as sponges, sea squirts, corals, worms and algae host diverse and abundant symbiotic microorganisms. Marine microbial symbionts are possible the true producers or take part in the biosynthesis of some bioactive marine natural products isolated from the marine organism hosts. Investigation of the pharmaceutical metabolites may reveal the biosynthesis mechanisms of related natural products and solve the current problem of supply limitation in marine drug development. This paper reviews the advances in diversity revelation, biological activity and related pharmaceutical metabolites, and functional genes of marine microbial symbionts from the China Sea.

  10. Microbial Diversity in Extreme Marine Habitats and Their Biomolecules.

    Science.gov (United States)

    Poli, Annarita; Finore, Ilaria; Romano, Ida; Gioiello, Alessia; Lama, Licia; Nicolaus, Barbara

    2017-05-16

    Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.

  11. Low-molecular-weight hydroxyacids in marine atmospheric aerosol: evidence of a marine microbial origin

    Science.gov (United States)

    Miyazaki, Y.; Sawano, M.; Kawamura, K.

    2014-08-01

    Lactic acid (LA) and glycolic acid (GA), which are low-molecular-weight hydroxyacids, were identified in the particle and gas phases within the marine atmospheric boundary layer over the western subarctic North Pacific. A major portion of LA (81%) and GA (57%) was present in the particulate phase, which is consistent with the presence of a hydroxyl group in these molecules leading to the low volatility of the compounds. The average concentration (±SD) of LA in more biologically influenced marine aerosols (33 ± 58 ng m-3) was substantially higher than that in less biologically influenced aerosols (11 ± 12 ng m-3). Over the oceanic region of phytoplankton blooms, the concentration of aerosol LA was comparable to that of oxalic acid, which was the most abundant diacid during the study period. A positive correlation was found between the LA concentrations in more biologically influenced aerosols and chlorophyll a in seawater (r2 = 0.56), suggesting an important production of aerosol LA possibly associated with microbial (e.g., lactobacillus) activity in seawater and/or aerosols. Our finding provides a new insight into the poorly quantified microbial sources of marine organic aerosols (OAs) because such low-molecular-weight hydroxyacids are key intermediates for OA formation.

  12. Thermophilic anaerobic oxidation of methane by marine microbial consortia.

    Science.gov (United States)

    Holler, Thomas; Widdel, Friedrich; Knittel, Katrin; Amann, Rudolf; Kellermann, Matthias Y; Hinrichs, Kai-Uwe; Teske, Andreas; Boetius, Antje; Wegener, Gunter

    2011-12-01

    The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. AOM is performed by microbial consortia of archaea (ANME) associated with partners related to sulfate-reducing bacteria. In vitro enrichments of AOM were so far only successful at temperatures ≤25 °C; however, energy gain for growth by AOM with sulfate is in principle also possible at higher temperatures. Sequences of 16S rRNA genes and core lipids characteristic for ANME as well as hints of in situ AOM activity were indeed reported for geothermally heated marine environments, yet no direct evidence for thermophilic growth of marine ANME consortia was obtained to date. To study possible thermophilic AOM, we investigated hydrothermally influenced sediment from the Guaymas Basin. In vitro incubations showed activity of sulfate-dependent methane oxidation between 5 and 70 °C with an apparent optimum between 45 and 60 °C. AOM was absent at temperatures ≥75 °C. Long-term enrichment of AOM was fastest at 50 °C, yielding a 13-fold increase of methane-dependent sulfate reduction within 250 days, equivalent to an apparent doubling time of 68 days. The enrichments were dominated by novel ANME-1 consortia, mostly associated with bacterial partners of the deltaproteobacterial HotSeep-1 cluster, a deeply branching phylogenetic group previously found in a butane-amended 60 °C-enrichment culture of Guaymas sediments. The closest relatives (Desulfurella spp.; Hippea maritima) are moderately thermophilic sulfur reducers. Results indicate that AOM and ANME archaea could be of biogeochemical relevance not only in cold to moderate but also in hot marine habitats.

  13. Assessing Marine Microbial Induced Corrosion at Santa Catalina Island, California.

    Science.gov (United States)

    Ramírez, Gustavo A; Hoffman, Colleen L; Lee, Michael D; Lesniewski, Ryan A; Barco, Roman A; Garber, Arkadiy; Toner, Brandy M; Wheat, Charles G; Edwards, Katrina J; Orcutt, Beth N

    2016-01-01

    High iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, CA, USA, for periods of 2 and 6 months. Substrates consisted of mild steel - a major constituent of maritime infrastructure - and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting "high-flux" conditions; a "stagnant" condition; an "active" flow-through condition with seawater slowly pumped over the substrates; and an "enrichment" condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the 2-month high flux incubations document coating of substrates with "twisted stalks," resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria (FeOB). Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all 6 month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that (i) high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of marine neutrophilic Fe

  14. Assessing marine microbial induced corrosion at Santa Catalina Island, California

    Directory of Open Access Journals (Sweden)

    Gustavo Antonio Ramírez

    2016-10-01

    Full Text Available High iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial-induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, California, USA, for periods of two and six months. Substrates consisted of mild steel – a major constituent of maritime infrastructure – and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting high-flux conditions; a stagnant condition; an active flow-through condition with seawater slowly pumped over the substrates; and an enrichment condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the two-month high flux incubations document coating of substrates with twisted stalks, resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria. Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all six month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that i high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of

  15. Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments.

    Science.gov (United States)

    Brandt, Leah D; House, Christopher H

    2016-01-01

    Sediments within the Okinawa back-arc basin overlay a subsurface hydrothermal network, creating intense temperature gradients with sediment depth and potential limits for microbial diversity. We investigated taxonomic changes across 45 m of recovered core with a temperature gradient of 3°C/m from the dynamic Iheya North Hydrothermal System. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay at 10 meters below seafloor (mbsf). Here, we present taxonomic results from an analysis of the 16S rRNA gene that support a conceptual model in which common marine subsurface taxa persist into the subsurface, while high temperature adapted archaeal taxa show localized peaks in abundances in the hydrothermal clay horizons. Specifically, the bacterial phylum Chloroflexi accounts for a major proportion of the total microbial community within the upper 10 mbsf, whereas high temperature archaea (Terrestrial Hot Spring Crenarchaeotic Group and methanotrophic archaea) appear in varying local abundances in deeper, hydrothermal clay horizons with higher in situ temperatures (up to 55°C, 15 mbsf). In addition, geochemical evidence suggests that methanotrophy may be occurring in various horizons. There is also relict DNA (i.e., DNA preserved after cell death) that persists in horizons where the conditions suitable for microbial communities have ceased.

  16. The microbial nitrogen cycling potential in marine sediments is impacted by polyaromatic hydrocarbon pollution

    Directory of Open Access Journals (Sweden)

    Nicole M Scott

    2014-03-01

    Full Text Available During petroleum hydrocarbon exposure the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential, if the sediments are aerobic, within the surface layer of marine sediments resulting in anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. These data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.

  17. Marine sponges and their microbial symbionts: love and other relationships.

    Science.gov (United States)

    Webster, Nicole S; Taylor, Michael W

    2012-02-01

    Many marine sponges harbour dense and diverse microbial communities of considerable ecological and biotechnological importance. While the past decade has seen tremendous advances in our understanding of the phylogenetic diversity of sponge-associated microorganisms (more than 25 bacterial phyla have now been reported from sponges), it is only in the past 3-4 years that the in situ activity and function of these microbes has become a major research focus. Already the rewards of this new emphasis are evident, with genomics and experimental approaches yielding novel insights into symbiont function. Key steps in the nitrogen cycle [denitrification, anaerobic ammonium oxidation (Anammox)] have recently been demonstrated in sponges for the first time, with diverse bacteria - including the sponge-associated candidate phylum 'Poribacteria'- being implicated in these processes. In this minireview we examine recent major developments in the microbiology of sponges, and identify several research areas (e.g. biology of viruses in sponges, effects of environmental stress) that we believe are deserving of increased attention. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  18. The Role of the Horizontal Gene Pool and Lateral Gene Transfer in Enhancing Microbial Activities in Marine Sediments

    National Research Council Canada - National Science Library

    Sobecky, Patricia A

    2006-01-01

    To better understand plasmid distribution, diversity and abundance in marine sediment microbial communities we developed a number of methodological approaches to advance the field during this project...

  19. Evaluation of marine sediments as microbial sources for methane production from brown algae under high salinity.

    Science.gov (United States)

    Miura, Toyokazu; Kita, Akihisa; Okamura, Yoshiko; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Kato, Junichi; Nakashimada, Yutaka

    2014-10-01

    Various marine sediments were evaluated as promising microbial sources for methane fermentation of Saccharina japonica, a brown alga, at seawater salinity. All marine sediments tested produced mainly acetate among volatile fatty acids. One marine sediment completely converted the produced volatile fatty acids to methane in a short period. Archaeal community analysis revealed that acetoclastic methanogens belonging to the Methanosarcina genus dominated after cultivation. Measurement of the specific conversion rate at each step of methane production under saline conditions demonstrated that the marine sediments had higher conversion rates of butyrate and acetate than mesophilic methanogenic granules. These results clearly show that marine sediments can be used as microbial sources for methane production from algae under high-salt conditions without dilution. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.

    Science.gov (United States)

    Ten Hoopen, Petra; Pesant, Stéphane; Kottmann, Renzo; Kopf, Anna; Bicak, Mesude; Claus, Simon; Deneudt, Klaas; Borremans, Catherine; Thijsse, Peter; Dekeyzer, Stefanie; Schaap, Dick Ma; Bowler, Chris; Glöckner, Frank Oliver; Cochrane, Guy

    2015-01-01

    Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7(th) Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

  1. Climate change and the potential spreading of marine mucilage and microbial pathogens in the Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Roberto Danovaro

    2009-09-01

    Full Text Available Marine snow (small amorphous aggregates with colloidal properties is present in all oceans of the world. Surface water warming and the consequent increase of water column stability can favour the coalescence of marine snow into marine mucilage, large marine aggregates representing an ephemeral and extreme habitat. Marine mucilage characterize aquatic systems with altered environmental conditions.We investigated, by means of molecular techniques, viruses and prokaryotes within the mucilage and in surrounding seawater to examine the potential of mucilage to host new microbial diversity and/or spread marine diseases. We found that marine mucilage contained a large and unexpectedly exclusive microbial biodiversity and hosted pathogenic species that were absent in surrounding seawater. We also investigated the relationship between climate change and the frequency of mucilage in the Mediterranean Sea over the last 200 years and found that the number of mucilage outbreaks increased almost exponentially in the last 20 years. The increasing frequency of mucilage outbreaks is closely associated with the temperature anomalies.We conclude that the spreading of mucilage in the Mediterranean Sea is linked to climate-driven sea surface warming. The mucilage can act as a controlling factor of microbial diversity across wide oceanic regions and could have the potential to act as a carrier of specific microorganisms, thereby increasing the spread of pathogenic bacteria.

  2. Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

    OpenAIRE

    Marc Troussellier; Arthur Escalas; Thierry Bouvier; David Mouillot; David Mouillot

    2017-01-01

    Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be ne...

  3. Microbially influenced corrosion of stainless steel by marine bacterium Vibrio natriegens: (I) Corrosion behavior

    International Nuclear Information System (INIS)

    Cheng Sha; Tian Jintao; Chen Shougang; Lei Yanhua; Chang Xueting; Liu Tao; Yin Yansheng

    2009-01-01

    The microbially influenced corrosion of stainless steel (SS) by marine bacterium Vibrio natriegens (V. natriegens) was investigated using surface analysis (atomic force microscopy (AFM), scanning electron microscopy (SEM), and energy dispersive X-ray analysis (EDXA)) and electrochemical techniques (the open circuit potential, electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization curves ). AFM images corroborated the results from the EIS models which show biofilm attachment and subsequent detachment over time. The SEM images revealed the occurrence of micro-pitting corrosion underneath the biofilms on the metal surface after the biofilm removal. The presence of carbon, oxygen, phosphor and sulfur obtained from EDXA proved the formation of biofilm. The electrochemical results showed that the corrosion of SS was accelerated in the presence of V. natriegens based on the decrease in the resistance of the charge transfer resistance (R ct ) obtained from EIS and the increase in corrosion current densities obtained from potentiodynamic polarization curves.

  4. Scaling microbial physiology in global models (Invited)

    Science.gov (United States)

    Wieder, W. R.; Bonan, G. B.; Hinckley, E. S.; Allison, S. D.

    2013-12-01

    A growing chorus from the biogeochemistry, soil science, and ecosystem modeling communities calls for model structures that provide direct microbial control over soil C dynamics. Thus, we describe a new model that explicitly represents microbial physiology in its representation of soil C cycling on the global scale. Presently, the model is parameterized based on measurements of microbial enzyme kinetics, but we must make assumptions about other aspects of microbial physiology (e.g., microbial growth efficiency and microbial turnover rates). We demonstrate that, compared to traditional soil biogeochemistry modeling approaches, the microbial explicit model can simulate global soil C pools that more closely match contemporary observations (based on the Harmonized World Soils Database), but generate wildly divergent results in response to environmental perturbations. The discrepancy between projections in non-steady state simulations highlight the modeling processes, parameters, and structures that deserve greater attention from both empirical and modeling communities and provide avenues to begin exploring soil biogeochemical theory across spatial and temporal scales.

  5. Mathematical modeling of microbial growth in milk

    Directory of Open Access Journals (Sweden)

    Jhony Tiago Teleken

    2011-12-01

    Full Text Available A mathematical model to predict microbial growth in milk was developed and analyzed. The model consists of a system of two differential equations of first order. The equations are based on physical hypotheses of population growth. The model was applied to five different sets of data of microbial growth in dairy products selected from Combase, which is the most important database in the area with thousands of datasets from around the world, and the results showed a good fit. In addition, the model provides equations for the evaluation of the maximum specific growth rate and the duration of the lag phase which may provide useful information about microbial growth.

  6. Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

    Directory of Open Access Journals (Sweden)

    Marc Troussellier

    2017-05-01

    Full Text Available Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms. Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.

  7. Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity.

    Science.gov (United States)

    Troussellier, Marc; Escalas, Arthur; Bouvier, Thierry; Mouillot, David

    2017-01-01

    Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares , which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.

  8. The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

    Directory of Open Access Journals (Sweden)

    Maryam Yazdani Foshtomi

    Full Text Available The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.Our results indicated that bacteria (total and β-AOB showed more spatio-temporal variation than archaea (total and AOA as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal

  9. The role of coastal fog in increased viability of marine microbial aerosols

    Science.gov (United States)

    Dueker, M.; O'Mullan, G. D.; Weathers, K. C.; Juhl, A. R.; Uriarte, M.

    2011-12-01

    Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. Despite the ubiquity of these bacteria (concentration estimates range from 1 x 10^4 to 6 x 10^5 cells m-3), much is still being learned about their source, viability, and interactions with climatic controls. They can be attached to ambient aerosol particles or exist singly in the air. They affect climate by serving as ice, cloud, and fog nucleators, and have the metabolic potential to alter atmospheric chemistry. Fog presence in particular has been shown to greatly increase the deposition of viable microbial aerosols in both urban and coastal environments, but the mechanisms behind this are not fully understood. To address this gap, we examined the diversity of culturable microbial aerosols from a relatively pristine coastal environment in Maine (USA) and determined the effect of fog presence on viability and community composition of microbial aerosols. 16S rRNA sequencing of culturable ocean surface bacteria and depositing microbial aerosols (under clear and foggy conditions) resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium) making up 66% of all sequences. Seventy-five percent of the viable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. The fog and ocean surface sequence libraries were significantly more similar in microbial community composition than clear (non-foggy) and ocean surface libraries. These findings support a dual role for fog in enhancing the fallout of viable marine microbial aerosols via increased gravitational settling rates and decreased aerosolization stress on the organisms. The dominant presence of marine bacteria in coastal microbial aerosols provides a strong case for

  10. The microbial control of phosphorus fluxes in marine sediments

    NARCIS (Netherlands)

    Steenbergh, A.K.

    2012-01-01

    This thesis explores how microorganisms affect the release of the key nutrient phosphorus from marine sediments. A detailed understanding of the controls on regeneration of phosphorus from sediments is important because phosphorus availability in surface waters can regulate primary productivity.

  11. Microbial Bioremediation of Fuel Oil Hydrocarbons in Marine Environment

    OpenAIRE

    Sapna Pavitran; C.B. Jagtap; S. Bala Subramanian; Susan Titus; Pradeep Kumar; P.C. Deb

    2006-01-01

    Pollution in marine environment due to heavier petroleum products such as high-speeddiesel is known to take from days to months for complete natural remediation owing to its lowvolatility. For the survival of marine flora and fauna, it is important to control pollution causedby such recalcitrant and xenobiotic substances. Several petroleum hydrocarbons found in natureare toxic and recalcitrant. Therefore, pollution due to high-speed diesel is a cause of concern.The natural dispersion of high-...

  12. Improving Marine Ecosystem Models with Biochemical Tracers

    Science.gov (United States)

    Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

    2018-01-01

    Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

  13. Chemical Investigations of Marine Filamentous and Zoosporic Fungi and Studies in Marine Microbial Chemical Ecology

    OpenAIRE

    Jenkins, Kelly M.

    1998-01-01

    The natural products chemistry of marine microorganisms is an emerging area of organic chemistry with the aim of discovering novel secondary metabolites exhibiting both biomedical and ecological activities. While marine bacteria have proven to be a productive source of new natural products, there are many groups of marine microorganisms which have not been fully investigated. In particular, marine fungi represent an untapped and potentially novel source of bioactive secondary metabolites. Whi...

  14. SULFIDE OXIDATION UNDER OXYGEN LIMITATION BY A THIOBACILLUS-THIOPARUS ISOLATED FROM A MARINE MICROBIAL MAT

    NARCIS (Netherlands)

    VANDENENDE, FP; VANGEMERDEN, H

    1993-01-01

    The colorless sulfur bacterium Thiobacillus thioparus T5, isolated from a marine microbial mat, was grown in continuous culture under conditions ranging from sulfide limitation to oxygen limitation. Under sulfide-limiting conditions, sulfide was virtually completely oxidized to sulfate. Under

  15. ABUNDANCE AND SALT TOLERANCE OF OBLIGATELY AEROBIC, PHOTOTROPHIC BACTERIA IN A MARINE MICROBIAL MAT

    NARCIS (Netherlands)

    YURKOV, VV; VANGEMERDEN, H

    Data have been collected on the abundance of obligately aerobic, bacteriochlorophyll-a-containing bacteria in a marine microbial mat on the West Frisian Island of Texel, The Netherlands. Plate counts on media rich in organic matter revealed average numbers of 3*10(5).cm-3 sediment in the top 10 mm

  16. Plant Microbial Fuel Cells; a new marine energy source

    NARCIS (Netherlands)

    Strik, D.P.B.T.B.; Hamelers, H.V.M.; Helder, M.; Timmers, R.A.; Steinbusch, K.J.J.; Buisman, C.J.N.

    2011-01-01

    Worldwide there is need for more clean, renewable, sustainable energy. Plant microbial fuel cells (Plant- MFCs) generate in-situ green electricity(Strik, Hamelers et al. 2008). How does this work? By photosynthesis the plant is capturing solar energy which is transformed into chemical energy as

  17. Fermentation Technologies for the Optimization of Marine Microbial Exopolysaccharide Production

    OpenAIRE

    Finore, Ilaria; Di Donato, Paola; Mastascusa, Vincenza; Nicolaus, Barbara; Poli, Annarita

    2014-01-01

    In the last decades, research has focused on the capabilities of microbes to secrete exopolysaccharides (EPS), because these polymers differ from the commercial ones derived essentially from plants or algae in their numerous valuable qualities. These biopolymers have emerged as new polymeric materials with novel and unique physical characteristics that have found extensive applications. In marine microorganisms the produced EPS provide an instrument to survive in adverse conditions: They are ...

  18. Microbial communities in marine sediments modify success of an invasive macrophyte.

    Science.gov (United States)

    Gribben, Paul E; Nielsen, Shaun; Seymour, Justin R; Bradley, Daniel J; West, Matthew N; Thomas, Torsten

    2017-08-29

    Invasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marine sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrass Zostera capricorni and the invasive alga Caulerpa taxifolia and that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities in Z. capricorni sediments provide biotic resistance by reducing C. taxifolia fragment growth 119% compared to when they are inactive, and intact microbial communities in C. taxifolia sediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.

  19. Petroleum Oxidation in Marine Microcosms by Natural Microbial Assemblages

    Science.gov (United States)

    Wardlaw, G. D.; Reddy, C. M.; Nelson, R. K.; Ehrhardt, C. J.; Valentine, D. L.

    2006-12-01

    Millions of gallons of petroleum are emitted into marine environments each year and the oxidation of this oil by microbes is an important mechanism for mediating toxicity. In terms of quantity, petroleum is the most abundant organic pollutant impacting marine environments today. Recent advances in chromatography have led to the development of comprehensive two-dimensional gas chromatography (GC &GC). The acronym, GC GC, is used because orthogonal gas chromatographic separations are achieved in both analytical dimensions by using stationary phases with varying partitioning abilities and selectivity. This novel method has greatly expanded the analytical window of petroleum hydrocarbons and was used to track the loss of petroleum hydrocarbons in aerobic marine microcosm experiments. Sediment microcosms were composed of seawater and sediment collected from the Coal Oil Point (COP) seep field off the coast of Santa Barbara, CA. Oil collected directly from the reservoir underlying the seep field was added to each microcosm, and samples were incubated for one year. Net metabolism was tracked by quantifying oxygen consumption and carbon dioxide production. The loss of petroleum components was tracked with GC GC, whereas the bacterial and archaeal community structures were tracked using T-RFLP. Results of these incubation studies will be presented.

  20. Coupling of fog and marine microbial content in the near-shore coastal environment

    Directory of Open Access Journals (Sweden)

    M. E. Dueker

    2012-02-01

    Full Text Available Microbes in the atmosphere (microbial aerosols play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. However, the sources and environmental factors controlling the concentration, diversity, transport, and viability of microbial aerosols are poorly understood. This study examined culturable microbial aerosols from a coastal environment in Maine (USA and determined the effect of onshore wind speed and fog presence on deposition rate, source, and community composition. During fog events with low onshore winds (<2 m s−1 the near-shore deposition of microbial aerosols (microbial fallout decreased with increasing wind speeds, whereas microbial fallout rates under clear conditions and comparable low wind speeds showed no wind speed dependence. Mean aerosol particle size also increased with onshore wind speed when fog was present, indicating increased shoreward transport of larger aerosol particles. 16S rRNA sequencing of culturable ocean surface bacteria and microbial aerosols deposited onshore resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium making up 66 % of all sequences. The sequence library from microbial aerosol isolates, as with libraries found in other coastal/marine aerosol studies, was dominated at the phylum level by Proteobacteria, with additional representation from Firmicutes, Actinobacteria and Bacteroidetes. Seventy-five percent of the culturable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. Using a 97 % similarity cut-off, sequence libraries from ocean surface and fog isolates shared eight operational taxonomic units (OTU's in total, three of which were the most dominant OTU's in the library, representing large fractions of the ocean (28

  1. Fermentation Technologies for the Optimization of Marine Microbial Exopolysaccharide Production

    Directory of Open Access Journals (Sweden)

    Ilaria Finore

    2014-05-01

    Full Text Available In the last decades, research has focused on the capabilities of microbes to secrete exopolysaccharides (EPS, because these polymers differ from the commercial ones derived essentially from plants or algae in their numerous valuable qualities. These biopolymers have emerged as new polymeric materials with novel and unique physical characteristics that have found extensive applications. In marine microorganisms the produced EPS provide an instrument to survive in adverse conditions: They are found to envelope the cells by allowing the entrapment of nutrients or the adhesion to solid substrates. Even if the processes of synthesis and release of exopolysaccharides request high-energy investments for the bacterium, these biopolymers permit resistance under extreme environmental conditions. Marine bacteria like Bacillus, Halomonas, Planococcus, Enterobacter, Alteromonas, Pseudoalteromonas, Vibrio, Rhodococcus, Zoogloea but also Archaea as Haloferax and Thermococcus are here described as EPS producers underlining biopolymer hyperproduction, related fermentation strategies including the effects of the chemical composition of the media, the physical parameters of the growth conditions and the genetic and predicted experimental design tools.

  2. Fermentation technologies for the optimization of marine microbial exopolysaccharide production.

    Science.gov (United States)

    Finore, Ilaria; Di Donato, Paola; Mastascusa, Vincenza; Nicolaus, Barbara; Poli, Annarita

    2014-05-22

    In the last decades, research has focused on the capabilities of microbes to secrete exopolysaccharides (EPS), because these polymers differ from the commercial ones derived essentially from plants or algae in their numerous valuable qualities. These biopolymers have emerged as new polymeric materials with novel and unique physical characteristics that have found extensive applications. In marine microorganisms the produced EPS provide an instrument to survive in adverse conditions: They are found to envelope the cells by allowing the entrapment of nutrients or the adhesion to solid substrates. Even if the processes of synthesis and release of exopolysaccharides request high-energy investments for the bacterium, these biopolymers permit resistance under extreme environmental conditions. Marine bacteria like Bacillus, Halomonas, Planococcus, Enterobacter, Alteromonas, Pseudoalteromonas, Vibrio, Rhodococcus, Zoogloea but also Archaea as Haloferax and Thermococcus are here described as EPS producers underlining biopolymer hyperproduction, related fermentation strategies including the effects of the chemical composition of the media, the physical parameters of the growth conditions and the genetic and predicted experimental design tools.

  3. Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts

    Science.gov (United States)

    Macintyre, Lynsey; Zhang, Tong; Viegelmann, Christina; Juarez Martinez, Ignacio; Cheng, Cheng; Dowdells, Catherine; Abdelmohsen, Usama Ramadan; Gernert, Christine; Hentschel, Ute; Edrada-Ebel, RuAngelie

    2014-01-01

    Marine invertebrate-associated symbiotic bacteria produce a plethora of novel secondary metabolites which may be structurally unique with interesting pharmacological properties. Selection of strains usually relies on literature searching, genetic screening and bioactivity results, often without considering the chemical novelty and abundance of secondary metabolites being produced by the microorganism until the time-consuming bioassay-guided isolation stages. To fast track the selection process, metabolomic tools were used to aid strain selection by investigating differences in the chemical profiles of 77 bacterial extracts isolated from cold water marine invertebrates from Orkney, Scotland using liquid chromatography-high resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) spectroscopy. Following mass spectrometric analysis and dereplication using an Excel macro developed in-house, principal component analysis (PCA) was employed to differentiate the bacterial strains based on their chemical profiles. NMR 1H and correlation spectroscopy (COSY) were also employed to obtain a chemical fingerprint of each bacterial strain and to confirm the presence of functional groups and spin systems. These results were then combined with taxonomic identification and bioassay screening data to identify three bacterial strains, namely Bacillus sp. 4117, Rhodococcus sp. ZS402 and Vibrio splendidus strain LGP32, to prioritize for scale-up based on their chemically interesting secondary metabolomes, established through dereplication and interesting bioactivities, determined from bioassay screening. PMID:24905482

  4. Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges.

    Science.gov (United States)

    Zhang, Fan; Blasiak, Leah C; Karolin, Jan O; Powell, Ryan J; Geddes, Chris D; Hill, Russell T

    2015-04-07

    Marine sponges are major habitat-forming organisms in coastal benthic communities and have an ancient origin in evolution history. Here, we report significant accumulation of polyphosphate (polyP) granules in three common sponge species of the Caribbean coral reef. The identity of the polyP granules was confirmed by energy-dispersive spectroscopy (EDS) and by the fluorescence properties of the granules. Microscopy images revealed that a large proportion of microbial cells associated with sponge hosts contained intracellular polyP granules. Cyanobacterial symbionts cultured from sponges were shown to accumulate polyP. We also amplified polyphosphate kinase (ppk) genes from sponge DNA and confirmed that the gene was expressed. Based on these findings, we propose here a potentially important phosphorus (P) sequestration pathway through symbiotic microorganisms of marine sponges. Considering the widespread sponge population and abundant microbial cells associated with them, this pathway is likely to have a significant impact on the P cycle in benthic ecosystems.

  5. Marine microbiology: Microbial ecology of the Red Sea [Mikrobielle Ökologie des Roten Meeres

    KAUST Repository

    Stingl, Ulrich

    2012-10-01

    The Red Sea is an unusually harsh marine environment, characterized by high temperature and salinity. It also harbors some of the most extreme environments on earth, the Deep Sea Brine Pools. Here, we report on the microbial communities in these environments. The water column is dominated by SAR11 and Prochlorococcus, which have developed specific adaptations to withstand the conditions. The Brine Pools have only been poorly characterized so far, and only four pure cultures are described. © Springer-Verlag 2012.

  6. Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics'era.

    Science.gov (United States)

    Cravo-Laureau, Cristiana; Duran, Robert

    2014-01-01

    Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment's complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment's reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying "omics" approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we

  7. Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics.

    Science.gov (United States)

    Nieminen, T T; Koskinen, K; Laine, P; Hultman, J; Säde, E; Paulin, L; Paloranta, A; Johansson, P; Björkroth, J; Auvinen, P

    2012-07-02

    Most raw poultry sold in Finland at the retail level is mixed with marinades containing oil, sugar, spices and acetic acid and packaged under modified atmosphere. Premature spoilage of marinated poultry preparations has been observed and associated with high levels of Leuconostoc spp. in meat. In this study we investigated whether marination of broiler fillet strips increased the proportion of Leuconostoc spp. in the microbial communities. To obtain a comprehensive view of the microbiota, we sequenced total DNA and 16S rRNA gene amplicons from the microbial communities. The lactic acid bacterial communities were characterized also by identification of colonies. The results showed that marinade increased the proportions of the spoilage-associated Leuconostoc gasicomitatum in the communities as well as the proportions of Leuconostoc gelidum and Lactobacillus spp. The proportions of Carnobacterium, Vagococcus, Brochothrix thrermosphacta, Clostridium, Enterobacteriaceae and Vibrio were diminished in marinated meat. Analysis of 16S rRNA gene amplicons resulted in 312 and 284 operational taxonomical units (dissimilarity 0.03) in unmarinated and marinated meat, respectively, indicating that the meat communities were more diverse than hitherto shown. Metagenomic analysis revealed a number of bacterial taxa that have not been associated with late shelf-life meat before, including Vagococcus and Vibrio that belonged to the predominating part of the microbial community in unmarinated meat. According to the functional analysis of the metagenomes, the communities in both marinated and unmarinated poultry were characterized by high proportions (15.6% or 17.9%) of genes involved in carbohydrate metabolism. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Redox effects on the microbial degradation of refractory organic matter in marine sediments

    Science.gov (United States)

    Reimers, Clare E.; Alleau, Yvan; Bauer, James E.; Delaney, Jennifer; Girguis, Peter R.; Schrader, Paul S.; Stecher, Hilmar A.

    2013-11-01

    Microbially mediated reduction-oxidation (redox) reactions are often invoked as being the mechanisms by which redox state influences the degradation of sedimentary organic matter (OM) in the marine environment. To evaluate the effects of elevated, oscillating and reduced redox potentials on the fate of primarily aged, mineral-adsorbed OM contained in continental shelf sediments, we used microbial fuel cells to control redox state within and around marine sediments, without amending the sediments with reducing or oxidizing substances. We subsequently followed electron fluxes in the redox elevated and redox oscillating treatments, and related sediment chemical, isotopic and bacterial community changes to redox conditions over a 748-day experimental period. The electron fluxes of the elevated and oscillating redox cells were consistent with models of organic carbon (OC) oxidation with time-dependent first-order rate constants declining from 0.023 to 0.005 y-1, in agreement with rate constants derived from typical OC profiles and down core ages of offshore sediments, or from sulfate reduction rate measurements in similar sediments. Moreover, although cumulative electron fluxes were higher in the continuously elevated redox treatment, incremental rates of electron harvesting in the two treatments converged over the 2 year experiment. These similar rates were reflected in chemical indicators of OM metabolism such as dissolved OC and ammonia, and particulate OC concentrations, which were not significantly different among all treatments and controls over the experimental time-scale. In contrast, products of carbonate and opal dissolution and metal mobilization showed greater enrichments in sediments with elevated and oscillating redox states. Microbial community composition in anode biofilms and surrounding sediments was assessed via high-throughput 16S rRNA gene sequencing, and these analyses revealed that the elevated and oscillatory redox treatments led to the

  9. Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis.

    Science.gov (United States)

    Trindade-Silva, Amaro E; Rua, Cintia; Silva, Genivaldo G Z; Dutilh, Bas E; Moreira, Ana Paula B; Edwards, Robert A; Hajdu, Eduardo; Lobo-Hajdu, Gisele; Vasconcelos, Ana Tereza; Berlinck, Roberto G S; Thompson, Fabiano L

    2012-01-01

    The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

  10. Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

    Science.gov (United States)

    Trindade-Silva, Amaro E.; Rua, Cintia; Silva, Genivaldo G. Z.; Dutilh, Bas E.; Moreira, Ana Paula B.; Edwards, Robert A.; Hajdu, Eduardo; Lobo-Hajdu, Gisele; Vasconcelos, Ana Tereza; Berlinck, Roberto G. S.; Thompson, Fabiano L.

    2012-01-01

    The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome. PMID:22768320

  11. Recent Advances in the Discovery and Development of Marine Microbial Natural Products

    Directory of Open Access Journals (Sweden)

    Yong Wang

    2013-03-01

    Full Text Available Marine microbial natural products (MMNPs have attracted increasing attention from microbiologists, taxonomists, ecologists, agronomists, chemists and evolutionary biologists during the last few decades. Numerous studies have indicated that diverse marine microbes appear to have the capacity to produce an impressive array of MMNPs exhibiting a wide variety of biological activities such as antimicrobial, anti-tumor, anti-inflammatory and anti-cardiovascular agents. Marine microorganisms represent an underexplored reservoir for the discovery of MMNPs with unique scaffolds and for exploitation in the pharmaceutical and agricultural industries. This review focuses on MMNPs discovery and development over the past decades, including innovative isolation and culture methods, strategies for discovering novel MMNPs via routine screenings, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology. The potential problems and future directions for exploring MMNPs are also discussed.

  12. Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review

    Science.gov (United States)

    Hardoim, Cristiane C. P.; Costa, Rodrigo

    2014-01-01

    Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed. PMID:25272328

  13. Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review

    Directory of Open Access Journals (Sweden)

    Cristiane C. P. Hardoim

    2014-09-01

    Full Text Available Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.

  14. Coupling of fog and marine microbial content in the near-shore coastal environment

    Science.gov (United States)

    Dueker, M. E.; O'Mullan, G. D.; Weathers, K. C.; Juhl, A. R.; Uriarte, M.

    2012-02-01

    Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. However, the sources and environmental factors controlling the concentration, diversity, transport, and viability of microbial aerosols are poorly understood. This study examined culturable microbial aerosols from a coastal environment in Maine (USA) and determined the effect of onshore wind speed and fog presence on deposition rate, source, and community composition. During fog events with low onshore winds (sequencing of culturable ocean surface bacteria and microbial aerosols deposited onshore resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium) making up 66 % of all sequences. The sequence library from microbial aerosol isolates, as with libraries found in other coastal/marine aerosol studies, was dominated at the phylum level by Proteobacteria, with additional representation from Firmicutes, Actinobacteria and Bacteroidetes. Seventy-five percent of the culturable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. Using a 97 % similarity cut-off, sequence libraries from ocean surface and fog isolates shared eight operational taxonomic units (OTU's) in total, three of which were the most dominant OTU's in the library, representing large fractions of the ocean (28 %) and fog (21 %) libraries. The fog and ocean surface libraries were significantly more similar in microbial community composition than clear (non-foggy) and ocean surface libraries, according to both Jaccard and Sorenson indices. These findings provide the first evidence of a difference in community composition and microbial culturability of aerosols associated with fog compared to clear conditions. The data support a dual role for fog

  15. Microbial diversity in methane hydrate-bearing deep marine sediments core preserved in the original pressure.

    Science.gov (United States)

    Takahashi, Y.; Hata, T.; Nishida, H.

    2017-12-01

    In normal coring of deep marine sediments, the sampled cores are exposed to the pressure of the atmosphere, which results in dissociation of gas-hydrates and might change microbial diversity. In this study, we analyzed microbial composition in methane hydrate-bearing sediment core sampled and preserved by Hybrid-PCS (Pressure Coring System). We sliced core into three layers; (i) outside layer, which were most affected by drilling fluids, (ii) middle layer, and (iii) inner layer, which were expected to be most preserved as the original state. From each layer, we directly extracted DNA, and amplified V3-V4 region of 16S rRNA gene. We determined at least 5000 of nucleotide sequences of the partial 16S rDNA from each layer by Miseq (Illumina). In the all layers, facultative anaerobes, which can grow with or without oxygen because they can metabolize energy aerobically or anaerobically, were detected as majority. However, the genera which are often detected anaerobic environment is abundant in the inner layer compared to the outside layer, indicating that condition of drilling and preservation affect the microbial composition in the deep marine sediment core. This study was conducted as a part of the activity of the Research Consortium for Methane Hydrate Resources in Japan [MH21 consortium], and supported by JOGMEC (Japan Oil, Gas and Metals National Corporation). The sample was provided by AIST (National Institute of Advanced Industrial Science and Technology).

  16. State-Space Modelling in Marine Science

    DEFF Research Database (Denmark)

    Albertsen, Christoffer Moesgaard

    State-space models provide a natural framework for analysing time series that cannot be observed without error. This is the case for fisheries stock assessments and movement data from marine animals. In fisheries stock assessments, the aim is to estimate the stock size; however, the only data...... available is the number of fish removed from the population and samples on a small fraction of the population. In marine animal movement, accurate position systems such as GPS cannot be used. Instead, inaccurate alternative must be used yielding observations with large errors. Both assessment and individual...... animal movement models are important for management and conservation of marine animals. Consequently, models should be developed to be operational in a management context while adequately evaluating uncertainties in the models. This thesis develops state-space models using the Laplace approximation...

  17. A General Business Model for Marine Reserves

    Science.gov (United States)

    Sala, Enric; Costello, Christopher; Dougherty, Dawn; Heal, Geoffrey; Kelleher, Kieran; Murray, Jason H.; Rosenberg, Andrew A.; Sumaila, Rashid

    2013-01-01

    Marine reserves are an effective tool for protecting biodiversity locally, with potential economic benefits including enhancement of local fisheries, increased tourism, and maintenance of ecosystem services. However, fishing communities often fear short-term income losses associated with closures, and thus may oppose marine reserves. Here we review empirical data and develop bioeconomic models to show that the value of marine reserves (enhanced adjacent fishing + tourism) may often exceed the pre-reserve value, and that economic benefits can offset the costs in as little as five years. These results suggest the need for a new business model for creating and managing reserves, which could pay for themselves and turn a profit for stakeholder groups. Our model could be expanded to include ecosystem services and other benefits, and it provides a general framework to estimate costs and benefits of reserves and to develop such business models. PMID:23573192

  18. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

    Directory of Open Access Journals (Sweden)

    Jennifer B. Glass

    2015-09-01

    Full Text Available Iron (Fe and copper (Cu are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3-, NO2-, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8 occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

  19. Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota

    Science.gov (United States)

    Sassoubre, Lauren M.; Yamahara, Kevan M.

    2015-01-01

    Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources. PMID:25576619

  20. Microbial hitchhikers on marine plastic debris: Human exposure risks at bathing waters and beach environments.

    Science.gov (United States)

    Keswani, Anisha; Oliver, David M; Gutierrez, Tony; Quilliam, Richard S

    2016-07-01

    Marine plastic debris is well characterized in terms of its ability to negatively impact terrestrial and marine environments, endanger coastal wildlife, and interfere with navigation, tourism and commercial fisheries. However, the impacts of potentially harmful microorganisms and pathogens colonising plastic litter are not well understood. The hard surface of plastics provides an ideal environment for opportunistic microbial colonisers to form biofilms and might offer a protective niche capable of supporting a diversity of different microorganisms, known as the "Plastisphere". This biotope could act as an important vector for the persistence and spread of pathogens, faecal indicator organisms (FIOs) and harmful algal bloom species (HABs) across beach and bathing environments. This review will focus on the existent knowledge and research gaps, and identify the possible consequences of plastic-associated microbes on human health, the spread of infectious diseases and bathing water quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress.

    Science.gov (United States)

    Fan, Lu; Liu, Michael; Simister, Rachel; Webster, Nicole S; Thomas, Torsten

    2013-05-01

    Large-scale mortality of marine invertebrates is a major global concern for ocean ecosystems and many sessile, reef-building animals, such as sponges and corals, are experiencing significant declines through temperature-induced disease and bleaching. The health and survival of marine invertebrates is often dependent on intimate symbiotic associations with complex microbial communities, yet we have a very limited understanding of the detailed biology and ecology of both the host and the symbiont community in response to environmental stressors, such as elevated seawater temperatures. Here, we use the ecologically important sponge Rhopaloeides odorabile as a model to explore the changes in symbiosis during the development of temperature-induced necrosis. Expression profiling of the sponge host was examined in conjunction with the phylogenetic and functional structure and the expression profile of the symbiont community. Elevated temperature causes an immediate stress response in both the host and symbiont community, including reduced expression of functions that mediate their partnership. Disruption to nutritional interdependence and molecular interactions during early heat stress further destabilizes the holobiont, ultimately leading to the loss of archetypal sponge symbionts and the introduction of new microorganisms that have functional and expression profiles consistent with a scavenging lifestyle, a lack virulence functions and a high growth rate. Previous models have postulated various mechanisms of mortality and disease in marine invertebrates. Our study suggests that interruption of symbiotic interactions is a major determinant for mortality in marine sessile invertebrates. High symbiont specialization and low functional redundancy, thus make these holobionts extremely vulnerable to environmental perturbations, including climate change.

  2. Bioinactivation: Software for modelling dynamic microbial inactivation.

    Science.gov (United States)

    Garre, Alberto; Fernández, Pablo S; Lindqvist, Roland; Egea, Jose A

    2017-03-01

    This contribution presents the bioinactivation software, which implements functions for the modelling of isothermal and non-isothermal microbial inactivation. This software offers features such as user-friendliness, modelling of dynamic conditions, possibility to choose the fitting algorithm and generation of prediction intervals. The software is offered in two different formats: Bioinactivation core and Bioinactivation SE. Bioinactivation core is a package for the R programming language, which includes features for the generation of predictions and for the fitting of models to inactivation experiments using non-linear regression or a Markov Chain Monte Carlo algorithm (MCMC). The calculations are based on inactivation models common in academia and industry (Bigelow, Peleg, Mafart and Geeraerd). Bioinactivation SE supplies a user-friendly interface to selected functions of Bioinactivation core, namely the model fitting of non-isothermal experiments and the generation of prediction intervals. The capabilities of bioinactivation are presented in this paper through a case study, modelling the non-isothermal inactivation of Bacillus sporothermodurans. This study has provided a full characterization of the response of the bacteria to dynamic temperature conditions, including confidence intervals for the model parameters and a prediction interval of the survivor curve. We conclude that the MCMC algorithm produces a better characterization of the biological uncertainty and variability than non-linear regression. The bioinactivation software can be relevant to the food and pharmaceutical industry, as well as to regulatory agencies, as part of a (quantitative) microbial risk assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Computational modeling of synthetic microbial biofilms.

    Science.gov (United States)

    Rudge, Timothy J; Steiner, Paul J; Phillips, Andrew; Haseloff, Jim

    2012-08-17

    Microbial biofilms are complex, self-organized communities of bacteria, which employ physiological cooperation and spatial organization to increase both their metabolic efficiency and their resistance to changes in their local environment. These properties make biofilms an attractive target for engineering, particularly for the production of chemicals such as pharmaceutical ingredients or biofuels, with the potential to significantly improve yields and lower maintenance costs. Biofilms are also a major cause of persistent infection, and a better understanding of their organization could lead to new strategies for their disruption. Despite this potential, the design of synthetic biofilms remains a major challenge, due to the complex interplay between transcriptional regulation, intercellular signaling, and cell biophysics. Computational modeling could help to address this challenge by predicting the behavior of synthetic biofilms prior to their construction; however, multiscale modeling has so far not been achieved for realistic cell numbers. This paper presents a computational method for modeling synthetic microbial biofilms, which combines three-dimensional biophysical models of individual cells with models of genetic regulation and intercellular signaling. The method is implemented as a software tool (CellModeller), which uses parallel Graphics Processing Unit architectures to scale to more than 30,000 cells, typical of a 100 μm diameter colony, in 30 min of computation time.

  4. Microbial characterization of toluene-degrading denitrifying consortia obtained from terrestrial and marine ecosystems.

    Science.gov (United States)

    An, Y-J; Joo, Y-H; Hong, I-Y; Ryu, H-W; Cho, K-S

    2004-10-01

    The degradation characteristics of toluene coupled to nitrate reduction were investigated in enrichment culture and the microbial communities of toluene-degrading denitrifying consortia were characterized by denaturing gradient gel electrophoresis (DGGE) technique. Anaerobic nitrate-reducing bacteria were enriched from oil-contaminated soil samples collected from terrestrial (rice field) and marine (tidal flat) ecosystems. Enriched consortia degraded toluene in the presence of nitrate as a terminal electron acceptor. The degradation rate of toluene was affected by the initial substrate concentration and co-existence of other hydrocarbons. The types of toluene-degrading denitrifying consortia depended on the type of ecosystem. The clone RS-7 obtained from the enriched consortium of the rice field was most closely related to a toluene-degrading and denitrifying bacterium, Azoarcus denitrificians (A. tolulyticus sp. nov.). The clone TS-11 detected in the tidal flat enriched consortium was affiliated to Thauera sp. strain S2 (T. aminoaromatica sp. nov.) that was able to degrade toluene under denitrifying conditions. This indicates that environmental factors greatly influence microbial communities obtained from terrestrial (rice field) and marine (tidal flat) ecosystems.

  5. Genomic mining for novel FADH₂-dependent halogenases in marine sponge-associated microbial consortia.

    Science.gov (United States)

    Bayer, Kristina; Scheuermayer, Matthias; Fieseler, Lars; Hentschel, Ute

    2013-02-01

    Many marine sponges (Porifera) are known to contain large amounts of phylogenetically diverse microorganisms. Sponges are also known for their large arsenal of natural products, many of which are halogenated. In this study, 36 different FADH₂-dependent halogenase gene fragments were amplified from various Caribbean and Mediterranean sponges using newly designed degenerate PCR primers. Four unique halogenase-positive fosmid clones, all containing the highly conserved amino acid motif "GxGxxG", were identified in the microbial metagenome of Aplysina aerophoba. Sequence analysis of one halogenase-bearing fosmid revealed notably two open reading frames with high homologies to efflux and multidrug resistance proteins. Single cell genomic analysis allowed for a taxonomic assignment of the halogenase genes to specific symbiotic lineages. Specifically, the halogenase cluster S1 is predicted to be produced by a deltaproteobacterial symbiont and halogenase cluster S2 by a poribacterial sponge symbiont. An additional halogenase gene is possibly produced by an actinobacterial symbiont of marine sponges. The identification of three novel, phylogenetically, and possibly also functionally distinct halogenase gene clusters indicates that the microbial consortia of sponges are a valuable resource for novel enzymes involved in halogenation reactions.

  6. Elucidating Microbial Species-Specific Effects on Organic Matter Transformation in Marine Sediments

    Science.gov (United States)

    Mahmoudi, N.; Enke, T. N.; Beaupre, S. R.; Teske, A.; Cordero, O. X.; Pearson, A.

    2017-12-01

    Microbial transformation and decomposition of organic matter in sediments constitutes one of the largest fluxes of carbon in marine environments. Mineralization of sedimentary organic matter by microorganisms results in selective degradation such that bioavailable or accessible compounds are rapidly metabolized while more recalcitrant, complex compounds are preserved and buried in sediment. Recent studies have found that the ability to use different carbon sources appears to vary among microorganisms, suggesting that the availability of certain pools of carbon can be specific to the taxa that utilize the pool. This implies that organic matter mineralization in marine environments may depend on the metabolic potential of the microbial populations that are present and active. The goal of our study was to investigate the extent to which organic matter availability and transformation may be species-specific using sediment from Guaymas Basin (Gulf of California). We carried out time-series incubations using bacterial isolates and sterilized sediment in the IsoCaRB system which allowed us to measure the production rates and natural isotopic signatures (δ13C and Δ14C) of microbially-respired CO2. Separate incubations using two different marine bacterial isolates (Vibrio sp. and Pseudoalteromonas sp.) and sterilized Guaymas Basin sediment under oxic conditions showed that the rate and total quantity of organic matter metabolized by these two species differs. Approximately twice as much CO2 was collected during the Vibrio sp. incubation compared to the Pseudoalteromonas sp. incubation. Moreover, the rate at which organic matter was metabolized by the Vibrio sp. was much higher than the Pseudoalteromonas sp. indicating the intrinsic availability of organic matter in sediments may depend on the species that is present and active. Isotopic analyses of microbially respired CO2 will be used to constrain the type and age of organic matter that is accessible to each species

  7. Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters.

    Science.gov (United States)

    Oberbeckmann, Sonja; Loeder, Martin G J; Gerdts, Gunnar; Osborn, A Mark

    2014-11-01

    Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  8. Marine Model Trout Farms: developments in marine RAS

    DEFF Research Database (Denmark)

    Pedersen, Per Bovbjerg

    2011-01-01

    . This development and demonstration unit in commercial scale will during the next four years hopefully provide scientific and practical basis and support for further development in coming generations of Marine Model Trout Farms for large salmonids. The unit consist in the recirculation loop of one large fish tank......, nitrogen is removed in a full-scale experimental set-up where sludge from the drum filter is hydrolysed and the VFAs generated used as energy-source for the denitrification process in separate tanks/filters. Final polishing follows in a constructed wetland. For the first 2 years of operation production...... will be focussed on rainbow trout production, mimicking the typical Danish net cage farming cycle, where the cages are stocked with fish of 750 – 1,000 g in April/May and all harvested before Christmas weighing some 4 kg/pcs. During these two years important production parameters such as growth-rate, feed...

  9. A Chemoinformatics Approach to the Discovery of Lead-Like Molecules from Marine and Microbial Sources En Route to Antitumor and Antibiotic Drugs

    Science.gov (United States)

    Pereira, Florbela; Latino, Diogo A. R. S.; Gaudêncio, Susana P.

    2014-01-01

    The comprehensive information of small molecules and their biological activities in the PubChem database allows chemoinformatic researchers to access and make use of large-scale biological activity data to improve the precision of drug profiling. A Quantitative Structure–Activity Relationship approach, for classification, was used for the prediction of active/inactive compounds relatively to overall biological activity, antitumor and antibiotic activities using a data set of 1804 compounds from PubChem. Using the best classification models for antibiotic and antitumor activities a data set of marine and microbial natural products from the AntiMarin database were screened—57 and 16 new lead compounds for antibiotic and antitumor drug design were proposed, respectively. All compounds proposed by our approach are classified as non-antibiotic and non-antitumor compounds in the AntiMarin database. Recently several of the lead-like compounds proposed by us were reported as being active in the literature. PMID:24473174

  10. An autocatalytic kinetic model for describing microbial growth during fermentation.

    Science.gov (United States)

    Ibarz, Albert; Augusto, Pedro E D

    2015-01-01

    The mathematical modelling of the behaviour of microbial growth is widely desired in order to control, predict and design food and bioproduct processing, stability and safety. This work develops and proposes a new semi-empirical mathematical model, based on an autocatalytic kinetic, to describe the microbial growth through its biomass concentration. The proposed model was successfully validated using 15 microbial growth patterns, covering the three most important types of microorganisms in food and biotechnological processing (bacteria, yeasts and moulds). Its main advantages and limitations are discussed, as well as the interpretation of its parameters. It is shown that the new model can be used to describe the behaviour of microbial growth.

  11. Genome-scale biological models for industrial microbial systems.

    Science.gov (United States)

    Xu, Nan; Ye, Chao; Liu, Liming

    2018-04-01

    The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

  12. Data Assimilation in Marine Models

    DEFF Research Database (Denmark)

    Frydendall, Jan

    maximum likelihood framework. These issues are discussed in paper B. The third part of the thesis falls a bit out of the above context is work published in papers C, F. In the first paper, a simple data assimilation scheme was investigated to examine the potential benefits of incorporating a data......This thesis consists of six research papers published or submitted for publication in the period 2006-2009 together with a summary report. The main topics of this thesis are nonlinear data assimilation techniques and estimation in dynamical models. The focus has been on the nonlinear filtering...... techniques for large scale geophysical numerical models and making them feasible to work with in the data assimilation framework. The filtering techniques investigated are all Monte Carlo simulation based. Some very nice features that can be exploited in the Monte Carlo based data assimilation framework from...

  13. Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges

    Directory of Open Access Journals (Sweden)

    Ute Hentschel

    2012-05-01

    Full Text Available Genomic mining revealed one major nonribosomal peptide synthetase (NRPS phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis.

  14. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

    Science.gov (United States)

    Gilbert, Jack A; Field, Dawn; Huang, Ying; Edwards, Rob; Li, Weizhong; Gilna, Paul; Joint, Ian

    2008-08-22

    Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, approximately 91% of which were novel. This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities--if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.

  15. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

    Directory of Open Access Journals (Sweden)

    Jack A Gilbert

    2008-08-01

    Full Text Available Sequencing the expressed genetic information of an ecosystem (metatranscriptome can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities.We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92% versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, approximately 91% of which were novel.This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities--if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.

  16. Carbohydrate production by phytoplankton and degradation in the marine microbial food web

    NARCIS (Netherlands)

    Alderkamp, Anne-Carlijn

    2006-01-01

    In this PhD thesis I describe studies relating to the cycling of the algal storage glucan chrysolaminaran. Chrysolaminaran is the most abundant type of storage carbohydrate in marine phytoplankton. I choose it as a model substrate to study factors influencing the cycling of carbohydrates, one of the

  17. Global soil carbon projections are improved by modelling microbial processes

    Science.gov (United States)

    Wieder, William R.; Bonan, Gordon B.; Allison, Steven D.

    2013-10-01

    Society relies on Earth system models (ESMs) to project future climate and carbon (C) cycle feedbacks. However, the soil C response to climate change is highly uncertain in these models and they omit key biogeochemical mechanisms. Specifically, the traditional approach in ESMs lacks direct microbial control over soil C dynamics. Thus, we tested a new model that explicitly represents microbial mechanisms of soil C cycling on the global scale. Compared with traditional models, the microbial model simulates soil C pools that more closely match contemporary observations. It also projects a much wider range of soil C responses to climate change over the twenty-first century. Global soils accumulate C if microbial growth efficiency declines with warming in the microbial model. If growth efficiency adapts to warming, the microbial model projects large soil C losses. By comparison, traditional models project modest soil C losses with global warming. Microbes also change the soil response to increased C inputs, as might occur with CO2 or nutrient fertilization. In the microbial model, microbes consume these additional inputs; whereas in traditional models, additional inputs lead to C storage. Our results indicate that ESMs should simulate microbial physiology to more accurately project climate change feedbacks.

  18. Chlorination or monochloramination: Balancing the regulated trihalomethane formation and microbial inactivation in marine aquaculture waters

    KAUST Repository

    Sanawar, Huma

    2017-08-15

    Disinfection methods like chlorination are increasingly used to sanitize the water, equipment, tools and surfaces in aquaculture facilities. This is to improve water quality, and to maintain a hygienic environment for the well-being of aquatic organisms. However, chlorination can result in formation of regulated disinfection byproducts (DBPs) that can be carcinogenic and toxic. This study aims to evaluate if an optimal balance can be achieved between minimal regulated DBP formation and effective microbial inactivation with either chlorination or monochloramination for application in the Red Sea aquaculture waters. Upon chlorination, the concentration of total trihalomethanes (THMs), primarily bromoform, exceeded the regulatory limit of 80μg/L even at the lowest tested concentration of chlorine (1mg/L) and contact time (1h). Comparatively, regulated THMs concentration was only detectable at 30μg/L level in one of the three sets of monochloraminated marine aquaculture waters. The average log reduction of antibiotic-resistant bacteria (ARB) by chlorine ranged from 2.3-log to 3.2-log with different contact time. The average log reduction of ARB by monochloramine was comparatively lower at 1.9 to 2.9-log. Although viable Staphylococcus aureus was recovered from monochloraminated samples as opposed to chlorinated samples, the abundance of S. aureus was not high enough to result in any significant microbial risks. Both chlorination and monochloramination did not provide any significant improvement in the reduction of antibiotic resistance genes (ARGs). This study demonstrates that a systematic evaluation is needed to determine the optimal disinfectant required to balance both microbial and chemical risks. Compared to chlorine, monochloramine may be a more appropriate disinfection strategy for the treatment of aquaculture effluents prior to discharge or for recirculatory use in the aquaculture facility.

  19. Do associated microbial abundances impact marine demosponge pumping rates and tissue densities?

    Science.gov (United States)

    Weisz, Jeremy B; Lindquist, Niels; Martens, Christopher S

    2008-03-01

    The evolution of marine demosponges has led to two basic life strategies: one involving close associations with large and diverse communities of microorganisms, termed high microbial abundance (HMA) species, and one that is essentially devoid of associated microorganisms, termed low microbial abundance (LMA) species. This dichotomy has previously been suggested to correlate with morphological differences, with HMA species having a denser mesohyl and a more complex aquiferous systems composed of longer and narrower water canals that should necessitate slower seawater filtration rates. We measured mesohyl density for a variety of HMA and LMA sponges in the Florida Keys, and seawater pumping rates for a select group of these sponges using an in situ dye technique. HMA sponges were substantially denser than LMA species, and had per unit volume pumping rates 52-94% slower than the LMA sponges. These density and pumping rate differences suggest that evolutionary differences between HMA and LMA species may have resulted in profound morphological and physiological differences between the two groups. The LMA sponge body plan moves large quantities of water through their porous tissues allowing them to rapidly acquire the small particulate organic matter (POM) that supplies the majority of their nutritional needs. In contrast, the HMA sponge body plan is suited to host large and tightly packed communities of microorganisms and has an aquiferous system that increases contact time between seawater and the sponge/microbial consortium that feeds on POM, dissolved organic matter and the raw inorganic materials for chemolithotrophic sponge symbionts. The two evolutionary patterns represent different, but equally successful patterns and illustrate how associated microorganisms can potentially have substantial effects on host evolution.

  20. Semi-continuous methane production from undiluted brown algae using a halophilic marine microbial community.

    Science.gov (United States)

    Miura, Toyokazu; Kita, Akihisa; Okamura, Yoshiko; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Kato, Junichi; Nakashimada, Yutaka

    2016-01-01

    Acclimated marine sediment-derived culture was used for semi-continuous methane production from materials equivalent to raw brown algae, without dilution of salinity and without nutrient supply, under 3 consecutive conditions of varying organic loading rates (OLRs) and hydraulic retention time (HRT). Methane production was stable at 2.0gVS/kg/day (39-day HRT); however, it became unstable at 2.9gVS/kg/day (28-day HRT) due to acetate and propionate accumulation. OLR subsequently decreased to 1.7gVS/kg/day (46-day HRT), stabilizing methane production beyond steady state. Methane yield was above 300mL/g VS at all OLRs. These results indicated that the acclimated marine sediment culture was able to produce methane semi-continuously from raw brown algae without dilution and nutrient supply under steady state. Microbial community analysis suggested that hydrogenotrophic methanogens predominated among archaea during unstable methane production, implying a partial shift of the methanogenic pathway from acetoclastic methanogenesis to acetate oxidation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Rapid Reactivation of Cyanobacterial Photosynthesis and Migration upon Rehydration of Desiccated Marine Microbial Mats

    KAUST Repository

    Chennu, Arjun

    2015-12-24

    Desiccated cyanobacterial mats are the dominant biological feature in the Earth’s arid zones. While the response of desiccated cyanobacteria to rehydration is well-documented for terrestrial systems, information about the response in marine systems is lacking. We used high temporal resolution hyperspectral imaging, liquid chromatography, pulse-amplitude fluorometry, oxygen microsensors, and confocal laser microscopy to study this response in a desiccated microbial mat from Exmouth Gulf, Australia. During the initial 15 min after rehydration chlorophyll a concentrations increased 2–5 fold and cyanobacterial photosynthesis was re-established. Although the mechanism behind this rapid increase of chlorophyll a remains unknown, we hypothesize that it involves resynthesis from a precursor stored in desiccated cyanobacteria. The subsequent phase (15 min–48 h) involved migration of the reactivated cyanobacteria toward the mat surface, which led, together with a gradual increase in chlorophyll a, to a further increase in photosynthesis. We conclude that the response involving an increase in chlorophyll a and recovery of photosynthetic activity within minutes after rehydration is common for cyanobacteria from desiccated mats of both terrestrial and marine origin. However, the response of upward migration and its triggering factor appear to be mat-specific and likely linked to other factors.

  2. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics.......Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  3. Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments

    Directory of Open Access Journals (Sweden)

    Ashleigh R. Currie

    2017-08-01

    Full Text Available Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2 and elevated temperature (ambient +4°C on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA and bacterial nitrite reductase (nirS were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

  4. Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments.

    Science.gov (United States)

    Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik

    2017-01-01

    Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO 2 ) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase ( amoA ) and bacterial nitrite reductase ( nirS ) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO 2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes ( amoA and nirS ) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

  5. Modelling marine protected areas: insights and hurdles

    Science.gov (United States)

    Fulton, Elizabeth A.; Bax, Nicholas J.; Bustamante, Rodrigo H.; Dambacher, Jeffrey M.; Dichmont, Catherine; Dunstan, Piers K.; Hayes, Keith R.; Hobday, Alistair J.; Pitcher, Roland; Plagányi, Éva E.; Punt, André E.; Savina-Rolland, Marie; Smith, Anthony D. M.; Smith, David C.

    2015-01-01

    Models provide useful insights into conservation and resource management issues and solutions. Their use to date has highlighted conditions under which no-take marine protected areas (MPAs) may help us to achieve the goals of ecosystem-based management by reducing pressures, and where they might fail to achieve desired goals. For example, static reserve designs are unlikely to achieve desired objectives when applied to mobile species or when compromised by climate-related ecosystem restructuring and range shifts. Modelling tools allow planners to explore a range of options, such as basing MPAs on the presence of dynamic oceanic features, and to evaluate the potential future impacts of alternative interventions compared with ‘no-action’ counterfactuals, under a range of environmental and development scenarios. The modelling environment allows the analyst to test if indicators and management strategies are robust to uncertainties in how the ecosystem (and the broader human–ecosystem combination) operates, including the direct and indirect ecological effects of protection. Moreover, modelling results can be presented at multiple spatial and temporal scales, and relative to ecological, economic and social objectives. This helps to reveal potential ‘surprises', such as regime shifts, trophic cascades and bottlenecks in human responses. Using illustrative examples, this paper briefly covers the history of the use of simulation models for evaluating MPA options, and discusses their utility and limitations for informing protected area management in the marine realm. PMID:26460131

  6. Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Gangsheng [ORNL; Mayes, Melanie [ORNL; Gu, Lianhong [ORNL; Schadt, Christopher Warren [ORNL

    2014-01-01

    Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in notable model uncertainties. To facilitate the consideration of dormancy in these large-scale models, we propose a new microbial physiology component that works for a wide range of substrate availabilities. This new model is based on microbial physiological states and the major parameters are the maximum specific growth and maintenance rates of active microbes and the ratio of dormant to active maintenance rates. A major improvement of our model over extant models is that it can explain the low active microbial fractions commonly observed in undisturbed soils. Our new model shows that the exponentially-increasing respiration from substrate-induced respiration experiments can only be used to determine the maximum specific growth rate and initial active microbial biomass, while the respiration data representing both exponentially-increasing and non-exponentially-increasing phases can robustly determine a range of key parameters including the initial total live biomass, initial active fraction, the maximum specific growth and maintenance rates, and the half-saturation constant. Our new model can be incorporated into existing ecosystem models to account for dormancy in microbially-driven processes and to provide improved estimates of microbial activities.

  7. Modelling microbial interactions and food structure in predictive microbiology

    NARCIS (Netherlands)

    Malakar, P.K.

    2002-01-01

    Keywords: modelling, dynamic models, microbial interactions, diffusion, microgradients, colony growth, predictive microbiology.

    Growth response of microorganisms in foods is a complex process. Innovations in food production and preservation techniques have resulted in adoption of

  8. Metabolic modeling to understand and redesign microbial systems

    NARCIS (Netherlands)

    Heck, van Ruben G.A.

    2017-01-01

    The goals of this thesis are to increase the understanding of microbial metabolism and to functionally (re-)design microbial systems using Genome- Scale Metabolic models (GSMs). GSMs are species-specific knowledge repositories that can be used to predict metabolic activities for wildtype and

  9. A Workflow to Model Microbial Loadings in Watersheds

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

  10. A Workflow to Model Microbial Loadings in Watersheds (proceedings)

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

  11. A Modeling Approach for Marine Observatory

    Directory of Open Access Journals (Sweden)

    Charbel Geryes Aoun

    2015-02-01

    Full Text Available Infrastructure of Marine Observatory (MO is an UnderWater Sensor Networks (UW-SN to perform collaborative monitoring tasks over a given area. This observation should take into consideration the environmental constraints since it may require specific tools, materials and devices (cables, servers, etc.. The logical and physical components that are used in these observatories provide data exchanged between the various devices of the environment (Smart Sensor, Data Fusion. These components provide new functionalities or services due to the long period running of the network. In this paper, we present our approach in extending the modeling languages to include new domain- specific concepts and constraints. Thus, we propose a meta-model that is used to generate a new design tool (ArchiMO. We illustrate our proposal with an example from the MO domain on object localization with several acoustics sensors. Additionally, we generate the corresponding simulation code for a standard network simulator using our self-developed domain-specific model compiler. Our approach helps to reduce the complexity and time of the design activity of a Marine Observatory. It provides a way to share the different viewpoints of the designers in the MO domain and obtain simulation results to estimate the network capabilities.

  12. Comparison of marine dispersion model predictions with environmental radionuclide concentrations

    International Nuclear Information System (INIS)

    Johnson, C.E.; McKay, W.A.

    1988-01-01

    The comparison of marine dispersion model results with measurements is an essential part of model development and testing. The results from two residual flow models are compared with seawater concentrations, and in one case with concentrations measured in marine molluscs. For areas with short turnover times, seawater concentrations respond rapidly to variations in discharge rate and marine currents. These variations are difficult to model, and comparison with concentrations in marine animals provides an alternative and complementary technique for model validation with the advantages that the measurements reflect the mean conditions and frequently form a useful time series. (author)

  13. Lagrangian Observations and Modeling of Marine Larvae

    Science.gov (United States)

    Paris, Claire B.; Irisson, Jean-Olivier

    2017-04-01

    Just within the past two decades, studies on the early-life history stages of marine organisms have led to new paradigms in population dynamics. Unlike passive plant seeds that are transported by the wind or by animals, marine larvae have motor and sensory capabilities. As a result, marine larvae have a tremendous capacity to actively influence their dispersal. This is continuously revealed as we develop new techniques to observe larvae in their natural environment and begin to understand their ability to detect cues throughout ontogeny, process the information, and use it to ride ocean currents and navigate their way back home, or to a place like home. We present innovative in situ and numerical modeling approaches developed to understand the underlying mechanisms of larval transport in the ocean. We describe a novel concept of a Lagrangian platform, the Drifting In Situ Chamber (DISC), designed to observe and quantify complex larval behaviors and their interactions with the pelagic environment. We give a brief history of larval ecology research with the DISC, showing that swimming is directional in most species, guided by cues as diverse as the position of the sun or the underwater soundscape, and even that (unlike humans!) larvae orient better and swim faster when moving as a group. The observed Lagrangian behavior of individual larvae are directly implemented in the Connectivity Modeling System (CMS), an open source Lagrangian tracking application. Simulations help demonstrate the impact that larval behavior has compared to passive Lagrangian trajectories. These methodologies are already the base of exciting findings and are promising tools for documenting and simulating the behavior of other small pelagic organisms, forecasting their migration in a changing ocean.

  14. Oxygen Minimum Zones in Miniature: Microbial Community Diversity, Activity, and Assembly Across Oxygen Gradients in Meromictic Marine Lakes, Palau

    Science.gov (United States)

    Beman, J. M.

    2016-02-01

    Oxygen minimum zones (OMZs) play a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet our understanding of these changes is limited by a lack of systematic analyses of low-oxygen ecosystems. In particular, forecasting biogeochemical feedbacks to deoxygenation requires detailed knowledge of microbial community assembly and activity as oxygen declines. Marine `lakes'—isolated bodies of seawater surrounded by land—are an ideal comparative system, as they provide a pronounced oxygen gradient extending from well-mixed, holomictic lakes to stratified, meromictic lakes that vary in their extent of anoxia. We examined 13 marine lakes using pyrosequencing of 16S rRNA genes, quantitative PCR for nitrogen (N)- and sulfur (S)-cycling functional genes and groups, and N- and carbon (C)-cycling rate measurements. All lakes were inhabited by well-known marine bacteria, demonstrating the broad relevance of this study system. Microbial diversity was typically highest in the anoxic monimolimnion of meromictic lakes, with marine cyanobacteria, SAR11, and other common bacteria replaced by anoxygenic phototrophs, sulfate-reducing bacteria (SRBs), and SAR406 in the monimolimnion. Denitrifier nitrite reductase (nirS) genes were also detected alongside high abundances (>106 ml-1) of dissimilatory sulfite reductase (dsrA) genes from SRBs in the monimolimnion. Sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis=76%) and deterministic processes dominated community assembly at all depths (nearest taxon index values >4). These results indicate that oxygen is a strong, deterministic driver of microbial community assembly. We also observed enhanced N- and C-cycling rates along the transition from hypoxic to anoxic to sulfidic conditions, suggesting that microbial communities form a positive feedback loop that may accelerate deoxygenation and OMZ expansion.

  15. In Situ Enhancement of Anaerobic Microbial Dechlorination of Polychlorinated Dibenzo-p-dioxins and Dibenzofurans in Marine and Estuarine Sediments

    Science.gov (United States)

    2006-12-18

    syringe. Butyric acid (440 :M) and pre- fermented yeast extract (4 :L of a 50 g/L solution) were added as electron donor and nutrient source...and pre- 18 fermented yeast extract were added at time zero and on day 8, 26, 120 and 178. Mixed cultures were agitated inverted at 200 rpm at 34 °C...In Situ Enhancement of Anaerobic Microbial Dechlorination of Polychlorinated Dibenzo-p-dioxins and Dibenzofurans in Marine and Estuarine

  16. Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events

    Directory of Open Access Journals (Sweden)

    Florent E. Angly

    2016-01-01

    Full Text Available The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR, with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae and Synechococcales (e.g., Prochlorococcus, and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.

  17. Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

    Energy Technology Data Exchange (ETDEWEB)

    Briggs, Brandon R; Graw, Michael; Brodie, Eoin L; Bahk, Jang-Jun; Kim, Sung-Han; Hyun, Jung-Ho; Kim, Ji-Hoon; Torres, Marta; Colwell, Frederick S

    2013-11-01

    The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining the results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.

  18. Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events.

    Science.gov (United States)

    Angly, Florent E; Heath, Candice; Morgan, Thomas C; Tonin, Hemerson; Rich, Virginia; Schaffelke, Britta; Bourne, David G; Tyson, Gene W

    2016-01-01

    The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010-11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.

  19. A Tropical Marine Microbial Natural Products Geobibliography as an Example of Desktop Exploration of Current Research Using Web Visualisation Tools

    Directory of Open Access Journals (Sweden)

    Elizabeth A. Evans-Illidge

    2008-10-01

    Full Text Available Microbial marine biodiscovery is a recent scientific endeavour developing at a time when information and other technologies are also undergoing great technical strides. Global visualisation of datasets is now becoming available to the world through powerful and readily available software such as Worldwind ™, ArcGIS Explorer ™ and Google Earth ™. Overlaying custom information upon these tools is within the hands of every scientist and more and more scientific organisations are making data available that can also be integrated into these global visualisation tools. The integrated global view that these tools enable provides a powerful desktop exploration tool. Here we demonstrate the value of this approach to marine microbial biodiscovery by developing a geobibliography that incorporates citations on tropical and near-tropical marine microbial natural products research with Google Earth ™ and additional ancillary global data sets. The tools and software used are all readily available and the reader is able to use and install the material described in this article.

  20. Rapid reactivation of cyanobacterial photosynthesis and migration upon rehydration of desiccated marine microbial mats

    Directory of Open Access Journals (Sweden)

    Arjun eChennu

    2015-12-01

    Full Text Available Desiccated cyanobacterial mats are the dominant biological feature in the Earth's arid zones. While the response of desiccated cyanobacteria to rehydration is well documented for terrestrial systems, information about the response in marine systems is lacking. We used high temporal resolution hyperspectral imaging, liquid chromatography, pulse-amplitude fluorometry, oxygen microsensors and confocal laser microscopy to study this response in a desiccated microbial mat from Exmouth Gulf, Australia. During the initial 15 minutes after rehydration chlorophyll a concentrations increased 2-5 fold and cyanobacterial photosynthesis was re-established. Although the mechanism behind this rapid increase of chlorophyll a remains unknown, we hypothesize that it involves resynthesis from a precursor stored in desiccated cyanobacteria. The subsequent phase (15 min – 48 h involved migration of the reactivated cyanobacteria towards the mat surface, which led, together with a gradual increase in chlorophyll a, to a further increase in photosynthesis. We conclude that the response involving an increase in chlorophyll a and recovery of photosynthetic activity within minutes after rehydration is common for cyanobacteria from desiccated mats of both terrestrial and aquatic origin. However the response of upward migration and its triggering factor appears to be mat-specific and likely linked to other factors.

  1. Modeling adaptation of carbon use efficiency in microbial communities

    Directory of Open Access Journals (Sweden)

    Steven D Allison

    2014-10-01

    Full Text Available In new microbial-biogeochemical models, microbial carbon use efficiency (CUE is often assumed to decline with increasing temperature. Under this assumption, soil carbon losses under warming are small because microbial biomass declines. Yet there is also empirical evidence that CUE may adapt (i.e. become less sensitive to warming, thereby mitigating negative effects on microbial biomass. To analyze potential mechanisms of CUE adaptation, I used two theoretical models to implement a tradeoff between microbial uptake rate and CUE. This rate-yield tradeoff is based on thermodynamic principles and suggests that microbes with greater investment in resource acquisition should have lower CUE. Microbial communities or individuals could adapt to warming by reducing investment in enzymes and uptake machinery. Consistent with this idea, a simple analytical model predicted that adaptation can offset 50% of the warming-induced decline in CUE. To assess the ecosystem implications of the rate-yield tradeoff, I quantified CUE adaptation in a spatially-structured simulation model with 100 microbial taxa and 12 soil carbon substrates. This model predicted much lower CUE adaptation, likely due to additional physiological and ecological constraints on microbes. In particular, specific resource acquisition traits are needed to maintain stoichiometric balance, and taxa with high CUE and low enzyme investment rely on low-yield, high-enzyme neighbors to catalyze substrate degradation. In contrast to published microbial models, simulations with greater CUE adaptation also showed greater carbon storage under warming. This pattern occurred because microbial communities with stronger CUE adaptation produced fewer degradative enzymes, despite increases in biomass. Thus the rate-yield tradeoff prevents CUE adaptation from driving ecosystem carbon loss under climate warming.

  2. Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia).

    Science.gov (United States)

    Zouch, Hana; Karray, Fatma; Armougom, Fabrice; Chifflet, Sandrine; Hirschler-Réa, Agnès; Kharrat, Hanen; Kamoun, Lotfi; Ben Hania, Wajdi; Ollivier, Bernard; Sayadi, Sami; Quéméneur, Marianne

    2017-01-01

    Anaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ~3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate) and sulfate sources (i.e., sodium sulfate or PG) as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia). Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria . When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures) was associated with an increase in the population of Firmicutes . These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.

  3. Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia

    Directory of Open Access Journals (Sweden)

    Hana Zouch

    2017-08-01

    Full Text Available Anaerobic biotechnology using sulfate-reducing bacteria (SRB is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG, an acidic (pH ~3 by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate and sulfate sources (i.e., sodium sulfate or PG as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia. Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.

  4. Bio-rescue of marine environments: On the track of microbially-based metal/metalloid remediation.

    Science.gov (United States)

    Marques, Catarina R

    2016-09-15

    The recent awareness of the huge relevance of marine resources and ecological services is driving regulatory demands for their protection from overwhelming contaminants, such as metals/metalloids. These contaminants enter and accumulate in different marine niches, hence deeply compromising their quality and integrity. Bioremediation has been flourishing to counteract metal/metalloid impacts, since it provides cost-effective and sustainable options by relying on ecology-based technologies. The potential of marine microbes for metal/metalloid bioremediation is the core of many studies, due to their high plasticity to overcome successive environmental hurdles. However, any thorough review on the advances of metal/metalloid bioremediation in marine environments was so far unveiled. This review is designed to (i) outline the characteristics and potential of marine microbes for metal/metalloid bioremediation, (ii) describe the underlying pathways of resistance and detoxification, as well as useful methodologies for their characterization, (iii) identify major bottlenecks on metal/metalloid bioremediation with marine microbes, (iv) present alternative strategies based on microbial consortia and engineered microbes for enhanced bioremediation, and (v) propose key research avenues to keep pace with a changing society, science and economy in a sustainable manner. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment.

    Science.gov (United States)

    Kevorkian, Richard; Bird, Jordan T; Shumaker, Alexander; Lloyd, Karen G

    2018-01-01

    growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community. IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes. Copyright © 2017 American Society for Microbiology.

  6. Acclimation of a marine microbial consortium for efficient Mn(II) oxidation and manganese containing particle production

    International Nuclear Information System (INIS)

    Zhou, Hao; Pan, Haixia; Xu, Jianqiang; Xu, Weiping; Liu, Lifen

    2016-01-01

    Highlights: • An efficient Mn(II) oxidation marine sediments microbial community was obtained. • High-throughput sequencing indicated new Mn(II) oxidation associated genus. • Na 3 MnPO 4 CO 3 and MnCO 3 were synthesized by the consortium. • Consortium exhibited Mn(II) oxidation performance over a range of harsh conditions. - Abstract: Sediment contamination with metals is a widespread concern in the marine environment. Manganese oxidizing bacteria (MOB) are extensively distributed in various environments, but a marine microbial community containing MOB is rarely reported. In this study, a consortium of marine metal-contaminated sediments was acclimated using Mn(II). The shift in community structure was determined through high-throughput sequencing. In addition, the consortium resisted several harsh conditions, such as toxic metals (1 mM Cu(II) and Fe(III)), and exhibited high Mn(II) oxidation capacities even the Mn(II) concentration was up to 5 mM. Meanwhile, biogenic Mn containing particles were characterized by scanning electron microscope (SEM), X-ray powder diffraction (XRD), and N 2 adsorption/desorption. Dye removal performance of the Mn containing particles was assayed using methylene blue, and 20.8 mg g −1 adsorption capacity was obtained. Overall, this study revealed several new genera associated with Mn(II) oxidation and rare biogenic Na 3 MnPO 4 CO 3. Results suggested the complexity of natural microbe-mediated Mn transformation.

  7. Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

    Science.gov (United States)

    Blatter, Maxime; Sugnaux, Marc; Comninellis, Christos; Nealson, Kenneth; Fischer, Fabian

    2016-07-07

    A predictive model for the microbial/electrochemical base formation from wastewater was established and compared to experimental conditions within a microbial electrolysis cell. A Na2 SO4 /K2 SO4 anolyte showed that model prediction matched experimental results. Using Shewanella oneidensis MR-1, a strong base (pH≈13) was generated using applied voltages between 0.3 and 1.1 V. Due to the use of bicarbonate, the pH value in the anolyte remained unchanged, which is required to maintain microbial activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Design, Modeling, and Development of Microbial Cell Factories

    KAUST Repository

    Kodzius, Rimantas

    2014-03-26

    Using Metagenomic analysis, computational modeling, single cell and genome editing technologies, we will express desired microbial genes and their networks in suitable hosts for mass production of energy, food, and fine chemicals.

  9. Modeling and Analysis in Marine Big Data: Advances and Challenges

    Directory of Open Access Journals (Sweden)

    Dongmei Huang

    2015-01-01

    Full Text Available It is aware that big data has gathered tremendous attentions from academic research institutes, governments, and enterprises in all aspects of information sciences. With the development of diversity of marine data acquisition techniques, marine data grow exponentially in last decade, which forms marine big data. As an innovation, marine big data is a double-edged sword. On the one hand, there are many potential and highly useful values hidden in the huge volume of marine data, which is widely used in marine-related fields, such as tsunami and red-tide warning, prevention, and forecasting, disaster inversion, and visualization modeling after disasters. There is no doubt that the future competitions in marine sciences and technologies will surely converge into the marine data explorations. On the other hand, marine big data also brings about many new challenges in data management, such as the difficulties in data capture, storage, analysis, and applications, as well as data quality control and data security. To highlight theoretical methodologies and practical applications of marine big data, this paper illustrates a broad view about marine big data and its management, makes a survey on key methods and models, introduces an engineering instance that demonstrates the management architecture, and discusses the existing challenges.

  10. A unique model system of microbial carbonate precipitation: Stromatolites of Lagoa Vermelha, Brazil

    Science.gov (United States)

    Warthmann, R. J.; Vasoncelos, C.; van Lith, Y.; Visscher, P. T.; McKenzie, J. A.

    2003-04-01

    Modern stromatolites are recognized as analogues to fossil laminated structures, which are remains of microbial activity that are widely found in sedimentary rocks beginning in the Neo-Archean, but are quite rare today. The key difference of modern microbial mats and stromatolites compared to ancient examples is the type of lithification. A few marine and hypersaline microbial mats have been observed to precipitate carbonates, and only in Shark Bay (Western, Australia) and Highborne Cay (Bahamas) has the formation of continuous laminae of carbonates been observed. Lagoa Vermelha, a moderate hypersaline lagoon in Rio de Janeiro, Brazil, offers the ideal conditions to promote lithification. Calcified, sometimes dolomitic stromatolites grow on the sediment surface, whereas within the sediments dolomite precipitates. The factors controlling carbonate precipitation in Lagoa Vermelha are the changing water chemistry and the special hydrology, combined with a high primary production by cyanobacteria, a high rate of respiration and the absence of higher organisms. Here, we present a study of the physico-chemical parameters, microbial processes and bio-minerals associated with these stromatolites and microbial mats. This approach provides boundary conditions to better understand dolomite formation. Several discrete lithified calcium carbonate layers are present. The first lithified layer is found beneath a 2-mm-thick biofilm, which contains Gloeocapsa. Below the underlying dense Microcoleus layer, the second micrite deposit is observed at 4-5 mm depth. Successive micritic laminae are preserved in the layer of decaying cyanobacteria that harbors large numbers of purple sulfur bacteria, heterotrophic microbes and sulfate-reducing bacteria. C-isotope studies of the carbonate layers indicate a contribution of organic derived carbon associated with microbial processes, such as sulfate reduction. The O-isotopic values indicate an evaporitic enrichment of the water. Understanding

  11. Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads

    KAUST Repository

    Gertler, Christoph

    2015-04-29

    Uric acid is a promising hydrophobic nitrogen source for biostimulation of microbial activities in oil-impacted marine environments. This study investigated metabolic processes and microbial community changes in a series of microcosms using sediment from the Mediterranean and the Red Sea amended with ammonium and uric acid. Respiration, emulsification, ammonium and protein concentration measurements suggested a rapid production of ammonium from uric acid accompanied by the development of microbial communities containing hydrocarbonoclastic bacteria after 3 weeks of incubation. About 80 % of uric acid was converted to ammonium within the first few days of the experiment. Microbial population dynamics were investigated by Ribosomal Intergenic Spacer Analysis and Illumina sequencing as well as by culture-based techniques. Resulting data indicated that strains related to Halomonas spp. converted uric acid into ammonium, which stimulated growth of microbial consortia dominated by Alcanivorax spp. and Pseudomonas spp. Several strains of Halomonas spp. were isolated on uric acid as the sole carbon source showed location specificity. These results point towards a possible role of halomonads in the conversion of uric acid to ammonium utilized by hydrocarbonoclastic bacteria. © 2015 Springer Science+Business Media New York

  12. Novel lineage patterns from an automated water sampler to probe marine microbial biodiversity with ships of opportunity

    Science.gov (United States)

    Stern, Rowena F.; Picard, Kathryn T.; Hamilton, Kristina M.; Walne, Antony; Tarran, Glen A.; Mills, David; McQuatters-Gollop, Abigail; Edwards, Martin

    2015-09-01

    There is a paucity of data on long-term, spatially resolved changes in microbial diversity and biogeography in marine systems, and yet these organisms underpin fundamental ecological processes in the oceans affecting socio-economic values of the marine environment. We report results from a new autonomous Water and Microplankton Sampler (WaMS) that is carried within the Continuous Plankton Recorder (CPR). Whilst the CPR with its larger mesh size (270 μm), is designed to capture larger plankton, the WaMS was designed as an additional device to capture plankton below 50 μm and delicate larger species, often destroyed by net sampling methods. A 454 pyrosequencing and flow cytometric investigation of eukaryotic microbes using the partial 18S rDNA from thirteen WaMS samples collected over three months in the English Channel revealed a wide diversity of organisms. Alveolates, Fungi, and picoplanktonic Chlorophytes were the most common lineages captured despite the small sample volumes (200-250 ml). The survey also identified Cercozoa and MAST heterotrophic Stramenopiles, normally missed in microscopic-based plankton surveys. The most common was the likely parasitic LKM11 Rozellomycota lineage which comprised 43.2% of all reads and are rarely observed in marine pelagic surveys. An additional 9.5% of reads belonged to other parasitic lineages including marine Syndiniales and Ichthyosporea. Sample variation was considerable, indicating that microbial diversity is spatially or temporally patchy. Our study has shown that the WaMS sampling system is autonomous, versatile and robust, and due to its deployment on the established CPR network, is a cost-effective monitoring tool for microbial diversity for the detection of smaller and delicate taxa.

  13. Integrating microbial diversity in soil carbon dynamic models parameters

    Science.gov (United States)

    Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

    2015-04-01

    Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

  14. Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia

    Directory of Open Access Journals (Sweden)

    Axel eSchippers

    2012-01-01

    Full Text Available Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 meters below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises R/V Meteor 72/5 and 76/1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, CARD-FISH and quantitative real-time PCR (Q-PCR. Total cell counts decreased with depths from 109 – 1010 cells /mL at the sediment surface to 107 – 109 cells /mL below one meter depth. Based on CARD-FISH and Q-PCR analysis overall similar proportions of Bacteria and Archaea were determined. The down core quantitative distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes as well as functional genes involved in different biogeochemical processes was successfully revealed by Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were as highly abundant as Archaea and Bacteria, respectively. Less abundant but detectable in most of the samples in high gene copy numbers were Eukarya and the Fe(III- and Mn(IV-reducing bacterial group Geobacteriaceae (off Namibia as well as the functional genes cbbL encoding for the large subunit of Rubisco, the functional genes dsrA and aprA of sulfate-reducers and the gene mcrA of methanogens. Overall the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

  15. An enrichment of CRISPR and other defense-related features in marine sponge-associated microbial metagenomes

    Directory of Open Access Journals (Sweden)

    Hannes Horn

    2016-11-01

    Full Text Available Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defense is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. This study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.

  16. Dental Biofilm and Laboratory Microbial Culture Models for Cariology Research

    Directory of Open Access Journals (Sweden)

    Ollie Yiru Yu

    2017-06-01

    Full Text Available Dental caries form through a complex interaction over time among dental plaque, fermentable carbohydrate, and host factors (including teeth and saliva. As a key factor, dental plaque or biofilm substantially influence the characteristic of the carious lesions. Laboratory microbial culture models are often used because they provide a controllable and constant environment for cariology research. Moreover, they do not have ethical problems associated with clinical studies. The design of the microbial culture model varies from simple to sophisticated according to the purpose of the investigation. Each model is a compromise between the reality of the oral cavity and the simplification of the model. Researchers, however, can still obtain meaningful and useful results from the models they select. Laboratory microbial culture models can be categorized into a closed system and an open system. Models in the closed system have a finite supply of nutrients, and are also simple and cost-effective. Models in the open system enabled the supply of a fresh culture medium and the removal of metabolites and spent culture liquid simultaneously. They provide better regulation of the biofilm growth rate than the models in the closed system. This review paper gives an overview of the dental plaque biofilm and laboratory microbial culture models used for cariology research.

  17. Microbial colonization and degradation of polyethylene and biodegradable plastic bags in temperate fine-grained organic-rich marine sediments.

    Science.gov (United States)

    Nauendorf, Alice; Krause, Stefan; Bigalke, Nikolaus K; Gorb, Elena V; Gorb, Stanislav N; Haeckel, Matthias; Wahl, Martin; Treude, Tina

    2016-02-15

    To date, the longevity of plastic litter at the sea floor is poorly constrained. The present study compares colonization and biodegradation of plastic bags by aerobic and anaerobic benthic microbes in temperate fine-grained organic-rich marine sediments. Samples of polyethylene and biodegradable plastic carrier bags were incubated in natural oxic and anoxic sediments from Eckernförde Bay (Western Baltic Sea) for 98 days. Analyses included (1) microbial colonization rates on the bags, (2) examination of the surface structure, wettability, and chemistry, and (3) mass loss of the samples during incubation. On average, biodegradable plastic bags were colonized five times higher by aerobic and eight times higher by anaerobic microbes than polyethylene bags. Both types of bags showed no sign of biodegradation during this study. Therefore, marine sediment in temperate coastal zones may represent a long-term sink for plastic litter and also supposedly compostable material. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Acclimation of a marine microbial consortium for efficient Mn(II) oxidation and manganese containing particle production

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Hao, E-mail: zhouhao@dlut.edu.cn [Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Food and Environment, Dalian University of Technology, Panjin 124221 (China); Pan, Haixia [Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Food and Environment, Dalian University of Technology, Panjin 124221 (China); Xu, Jianqiang [School of Life Science and Medicine, Dalian University of Technology, Panjin 124221 (China); Xu, Weiping; Liu, Lifen [Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Food and Environment, Dalian University of Technology, Panjin 124221 (China)

    2016-03-05

    Highlights: • An efficient Mn(II) oxidation marine sediments microbial community was obtained. • High-throughput sequencing indicated new Mn(II) oxidation associated genus. • Na{sub 3}MnPO{sub 4}CO{sub 3} and MnCO{sub 3} were synthesized by the consortium. • Consortium exhibited Mn(II) oxidation performance over a range of harsh conditions. - Abstract: Sediment contamination with metals is a widespread concern in the marine environment. Manganese oxidizing bacteria (MOB) are extensively distributed in various environments, but a marine microbial community containing MOB is rarely reported. In this study, a consortium of marine metal-contaminated sediments was acclimated using Mn(II). The shift in community structure was determined through high-throughput sequencing. In addition, the consortium resisted several harsh conditions, such as toxic metals (1 mM Cu(II) and Fe(III)), and exhibited high Mn(II) oxidation capacities even the Mn(II) concentration was up to 5 mM. Meanwhile, biogenic Mn containing particles were characterized by scanning electron microscope (SEM), X-ray powder diffraction (XRD), and N{sub 2} adsorption/desorption. Dye removal performance of the Mn containing particles was assayed using methylene blue, and 20.8 mg g{sup −1} adsorption capacity was obtained. Overall, this study revealed several new genera associated with Mn(II) oxidation and rare biogenic Na{sub 3}MnPO{sub 4}CO{sub 3.} Results suggested the complexity of natural microbe-mediated Mn transformation.

  19. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

    KAUST Repository

    Bayer, Kristina

    2015-01-08

    The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

  20. A generic view of classic microbial growth models.

    NARCIS (Netherlands)

    van den Berg, H.A.

    1998-01-01

    General theoretical aspects are reviewed of models for microbial growth and endogenous metabolism. The focus is on a generic cell model with two components. Growth is represented as the increase of one of these components (the structural scaffolding or 'frame'). A novel feature of the present

  1. Marine Subsurface Microbial Communities Across a Hydrothermal Gradient in Okinawa Trough Sediments

    Science.gov (United States)

    Brandt, L. D.; Hser Wah Saw, J.; Ettema, T.; House, C. H.

    2015-12-01

    IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 meters below sea floor (mbsf). Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 mbsf. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data shows a shift over 15 mbsf from a heterogeneous community of cosmopolitan marine subsurface taxa toward an archaeal-dominated community in the deepest horizons of the predicted biosphere. Notably, the phylum Chloroflexi represents a substantial taxon through most horizons, where it appears to be replaced below 10 mbsf by punctuations of thermophilic and methanotrophic Archaea and Miscellaneous Crenarchaeotic Group abundances. DNA from the aforementioned transition horizons was further analyzed using metagenomic sequencing. Preliminary taxonomic analysis of the metagenomic data agrees well with amplicon data in capturing the shift in relative abundance of Archaea increasing with depth. Additionally, reverse gyrase, a gene found exclusively in hyperthermophilic microorganisms, was recovered only in the metagenome of the deepest horizon. A BLAST search of this protein sequence against the GenBank non-redudnant protein database produced top hits with reverse gyrase from Thermococcus and Pyrococcus, which are

  2. Recent Advances in the Study of Marine Microbial Biofilm: From the Involvement of Quorum Sensing in Its Production up to Biotechnological Application of the Polysaccharide Fractions

    Directory of Open Access Journals (Sweden)

    Paola Di Donato

    2016-05-01

    Full Text Available The present review will explore the most relevant findings on marine microbial biofilm, with particular attention towards its polysaccharide fraction, namely exopolysaccharide (EPS. EPSs of microbial origin are ubiquitous in nature, possess unique properties and can be isolated from the bacteria living in a variety of habitats, including fresh water or marine environments, extreme environments or different soil ecosystems. These biopolymers have many application in the field of biotechnology. Several studies showed that the biofilm formation is closely related to quorum sensing (QS systems, which is a mechanism relying on the production of small molecules defined as “autoinducers” that bacteria release in the surrounding environment where they accumulate. In this review, the involvement of microbial chemical communication, by QS mechanism, in the formation of marine biofilm will also be discussed.

  3. Modeling microbial processes in porous media

    Science.gov (United States)

    Murphy, Ellyn M.; Ginn, Timothy R.

    The incorporation of microbial processes into reactive transport models has generally proceeded along two separate lines of investigation: (1) transport of bacteria as inert colloids in porous media, and (2) the biodegradation of dissolved contaminants by a stationary phase of bacteria. Research over the last decade has indicated that these processes are closely linked. This linkage may occur when a change in metabolic activity alters the attachment/detachment rates of bacteria to surfaces, either promoting or retarding bacterial transport in a groundwater-contaminant plume. Changes in metabolic activity, in turn, are controlled by the time of exposure of the microbes to electron acceptors/donor and other components affecting activity. Similarly, metabolic activity can affect the reversibility of attachment, depending on the residence time of active microbes. Thus, improvements in quantitative analysis of active subsurface biota necessitate direct linkages between substrate availability, metabolic activity, growth, and attachment/detachment rates. This linkage requires both a detailed understanding of the biological processes and robust quantitative representations of these processes that can be tested experimentally. This paper presents an overview of current approaches used to represent physicochemical and biological processes in porous media, along with new conceptual approaches that link metabolic activity with partitioning of the microorganism between the aqueous and solid phases. Résumé L'introduction des processus microbiologiques dans des modèles de transport réactif a généralement suivi deux voies différentes de recherches: (1) le transport de bactéries sous forme de colloïdes inertes en milieu poreux, et (2) la biodégradation de polluants dissous par une phase stationnaire de bactéries. Les recherches conduites au cours des dix dernières années indiquent que ces processus sont intimement liés. Cette liaison peut intervenir lorsqu

  4. Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions

    Energy Technology Data Exchange (ETDEWEB)

    López, José L.; Golemba, Marcelo; Hernández, Edgardo; Lozada, Mariana; Dionisi, Hebe; Jansson, Janet K.; Carroll, Jolynn; Lundgren, Leif; Sjöling, Sara; Mac Cormack, Walter P.; Sobecky, Patricia

    2016-11-03

    Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.

  5. Microbial Communities Model Parameter Calculation for TSPA/SR

    Energy Technology Data Exchange (ETDEWEB)

    D. Jolley

    2001-07-16

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M&O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M&O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow {Delta}G (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M&O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed.

  6. Modeling Studies on Microbial Effects on Groundwater Chemistry

    International Nuclear Information System (INIS)

    Yoshikatsu Tochigi; Hideki Yoshikawa; Mikazu Yui

    2007-01-01

    The overall goal of this project is to develop a model to predict microbial effects on the performance of a high-level radioactive waste (HLW) repository. As a first step, the effects of microbes on groundwater chemistry have been evaluated with the numerical code 'MINT', using data collected from the borehole HDB-6 in the Horonobe underground research laboratory (URL) in Japan. The MINT code models biochemistry and geochemical equilibrium, with consideration of transport of solute and microbial activity. The MINT code simulates the activities of six major groups of microbes, classified by their metabolism as 'aerobic', 'denitrifying', 'manganese reducing', 'iron reducing', 'sulfate reducing' and 'methanogenic'. The specific activity of each of these groups will depend on the redox potential (Eh) of the groundwater. Sensitivity analyses were performed to investigate the consequences of changes in groundwater composition on the effects of microbial activity. This indicates that the activities of Sulfate Reducing Bacteria (SRB) and methanogens are relatively high. The concentration of dissolved methane produced by such microbial activity is seen to be influenced by sulfate concentration. Based on the observed data from Horonobe URL, the concentration in oxygen is relatively high and the activity of denitrifying bacteria is the highest of the major six groups of microbes. This can, however, be attributable to chemical / microbial contamination of the groundwater during sampling. The modeling results indicate that the concentration of dissolved oxygen and nitrate ion should be quickly reduced by microbial metabolism, reducing the redox potential to a level low enough for active methano-genesis to commence. Such assessment can be important to evaluate the reliability of sampling and measurement techniques for sensitive geochemical parameters in general - and microbiology in particular. (authors)

  7. Microbial Communities Model Parameter Calculation for TSPA/SR

    International Nuclear Information System (INIS)

    D. Jolley

    2001-01-01

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M and O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M and O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow ΔG (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M and O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M and O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed

  8. B-Vitamin Competition: Intracellular and Dissolved B-Vitamins Provide Insight into Marine Microbial Community Dynamics

    Science.gov (United States)

    Suffridge, C.; Gomez-Consarnau, L.; Qu, P.; Tenenbaum, N.; Fu, F.; Hutchins, D. A.; Sanudo-Wilhelmy, S. A.

    2016-02-01

    The availability of B-vitamins has the ability to directly affect the dynamics of the marine microbial community. Here we show, for the first time, the connection between dissolved and intracellular B-vitamins in a marine environmental community. Two incubation experiments were conducted at a long-term study site (SPOT) in the San Pedro Basin off the coast of Los Angeles, CA. Experiments were conducted in oligotrophic, preupwelling conditions. Due to the 2015 El Niño event, the seasonal upwelling at SPOT did not occur, creating unusually nutrient depleted conditions. Vitamins B1, B7, and B12 were added in addition to macronutrients at concentrations similar to typical SPOT upwelling conditions. Intracellular and dissolved B-vitamin analyses were conducted to determine shifts in cellular B-vitamin requirements as a function of growth rate. We observed a significant bacterioplankton and phytoplankton growth responses with the addition of B-vitamins in a manner that appears to match the enzymatic requirements for these compounds (e.g. B1>B7>B12). Intracellular B-vitamin analysis of T0 samples support this observation, as all four forms of B12 were not detectable within cells, yet multiple forms of B1 and B7 were detected at or near levels previously reported. Treatments with B12 and macronutrients were observed to have the greatest growth rates. This finding, in addition to the apparent lack of intracellular B12 in the initial community, appears to indicate that the initial microbial community was limited by B12. The addition of each vitamin caused a distinct shift in the blooming microbial community. Our results demonstrate that B-vitamins strongly influence not only the growth rate, but also the species composition and species succession of the microbial community as a whole. Large-scale changes to upwelling regimes are predicted in the future ocean; our results indicate that B-vitamins will have a substantial role in controlling microbial community dynamics under

  9. Disruption of microbial biofilms by an extracellular protein isolated from epibiotic tropical marine strain of Bacillus licheniformis.

    Directory of Open Access Journals (Sweden)

    Devendra H Dusane

    Full Text Available BACKGROUND: Marine epibiotic bacteria produce bioactive compounds effective against microbial biofilms. The study examines antibiofilm ability of a protein obtained from a tropical marine strain of Bacillus licheniformis D1. METHODOLOGY/PRINCIPAL FINDINGS: B. licheniformis strain D1 isolated from the surface of green mussel, Perna viridis showed antimicrobial activity against pathogenic Candida albicans BH, Pseudomonas aeruginosa PAO1 and biofouling Bacillus pumilus TiO1 cultures. The antimicrobial activity was lost after treatment with trypsin and proteinase K. The protein was purified by ultrafiltration and size-exclusion chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF analysis revealed the antimicrobial agent to be a 14 kDa protein designated as BL-DZ1. The protein was stable at 75°C for 30 min and over a pH range of 3.0 to 11.0. The sequence alignment of the MALDI-fingerprint showed homology with the NCBI entry for a hypothetical protein (BL00275 derived from B. licheniformis ATCC 14580 with the accession number gi52082584. The protein showed minimum inhibitory concentration (MIC value of 1.6 µg/ml against C. albicans. Against both P. aeruginosa and B. pumilus the MIC was 3.12 µg/ml. The protein inhibited microbial growth, decreased biofilm formation and dispersed pre-formed biofilms of the representative cultures in polystyrene microtiter plates and on glass surfaces. CONCLUSION/SIGNIFICANCE: We isolated a protein from a tropical marine strain of B. licheniformis, assigned a function to the hypothetical protein entry in the NCBI database and described its application as a potential antibiofilm agent.

  10. Disruption of Microbial Biofilms by an Extracellular Protein Isolated from Epibiotic Tropical Marine Strain of Bacillus licheniformis

    Science.gov (United States)

    Dusane, Devendra H.; Damare, Samir R.; Nancharaiah, Yarlagadda V.; Ramaiah, N.; Venugopalan, Vayalam P.; Kumar, Ameeta Ravi; Zinjarde, Smita S.

    2013-01-01

    Background Marine epibiotic bacteria produce bioactive compounds effective against microbial biofilms. The study examines antibiofilm ability of a protein obtained from a tropical marine strain of Bacillus licheniformis D1. Methodology/Principal Findings B. licheniformis strain D1 isolated from the surface of green mussel, Perna viridis showed antimicrobial activity against pathogenic Candida albicans BH, Pseudomonas aeruginosa PAO1 and biofouling Bacillus pumilus TiO1 cultures. The antimicrobial activity was lost after treatment with trypsin and proteinase K. The protein was purified by ultrafiltration and size-exclusion chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis revealed the antimicrobial agent to be a 14 kDa protein designated as BL-DZ1. The protein was stable at 75°C for 30 min and over a pH range of 3.0 to 11.0. The sequence alignment of the MALDI-fingerprint showed homology with the NCBI entry for a hypothetical protein (BL00275) derived from B. licheniformis ATCC 14580 with the accession number gi52082584. The protein showed minimum inhibitory concentration (MIC) value of 1.6 µg/ml against C. albicans. Against both P. aeruginosa and B. pumilus the MIC was 3.12 µg/ml. The protein inhibited microbial growth, decreased biofilm formation and dispersed pre-formed biofilms of the representative cultures in polystyrene microtiter plates and on glass surfaces. Conclusion/Significance We isolated a protein from a tropical marine strain of B. licheniformis, assigned a function to the hypothetical protein entry in the NCBI database and described its application as a potential antibiofilm agent. PMID:23691235

  11. Development of a transport model for the microbial degradation of ...

    African Journals Online (AJOL)

    A mathematical model for first order reaction rate under isothermal condition was developed for predicting the diffusivity and transport rate of anthracene and pyrene during biodegradation using two microbial strains (corynebacteria spp and pseudomonas putida) in a heterogeneous porous medium. The formulation ...

  12. A Multiple Reaction Modelling Framework for Microbial Electrochemical Technologies

    Directory of Open Access Journals (Sweden)

    Tolutola Oyetunde

    2017-01-01

    Full Text Available A mathematical model for the theoretical evaluation of microbial electrochemical technologies (METs is presented that incorporates a detailed physico-chemical framework, includes multiple reactions (both at the electrodes and in the bulk phase and involves a variety of microbial functional groups. The model is applied to two theoretical case studies: (i A microbial electrolysis cell (MEC for continuous anodic volatile fatty acids (VFA oxidation and cathodic VFA reduction to alcohols, for which the theoretical system response to changes in applied voltage and VFA feed ratio (anode-to-cathode as well as membrane type are investigated. This case involves multiple parallel electrode reactions in both anode and cathode compartments; (ii A microbial fuel cell (MFC for cathodic perchlorate reduction, in which the theoretical impact of feed flow rates and concentrations on the overall system performance are investigated. This case involves multiple electrode reactions in series in the cathode compartment. The model structure captures interactions between important system variables based on first principles and provides a platform for the dynamic description of METs involving electrode reactions both in parallel and in series and in both MFC and MEC configurations. Such a theoretical modelling approach, largely based on first principles, appears promising in the development and testing of MET control and optimization strategies.

  13. Modeling Logistic Performance in Quantitative Microbial Risk Assessment

    NARCIS (Netherlands)

    Rijgersberg, H.; Tromp, S.O.; Jacxsens, L.; Uyttendaele, M.

    2010-01-01

    In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage

  14. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  15. Stochiometry, Microbial community composition and decomposition, a modelling analysis

    Science.gov (United States)

    Berninger, Frank; Zhou, Xuan; Aaltonen, Heidi; Köster, Kajar; Heinonsalo, Jussi; Pumpanen, Jukka

    2017-04-01

    Enzyme activity based litter decomposition models describe the decomposition of soil organic matter as a function of microbial biomass and its activity. In these models, decomposition depends largely on microbial and litter stoïchiometry. We, used the model of Schimel and Weintraub (Soil Biology & Biochemistry 35 (2003) 549-563 largely relying on the modification of Waring B et al. Ecology Letters, (2013) 16: 887-894) and we modified the model to include bacteria, fungi and mycorrizal fungi as decomposer groups assuming different stochiometries. The model was tested against previously published data from a fire chronosequence from northern Finland. The model reconstructed well the development of soil organic matter, microbial biomasses, enzyme actitivies with time after fire. In a theoretical model analysis we tried to understand how the exchange of carbon and nitrogen between mycorrhiza and the plant as different litter stoïchiometries interact. The results indicate that if a high percentage of fungal N uptake is transferred to the plant mycorrhizal biomass will decrease drastically and does decrease, due to low mycorrhizal biomasses, the N uptake of plants. If a lower proportion of the fungal N uptake is transferred to the plant the N uptake of the plants is reasonable stable while the proportion of mycorrhiza of the total fungal biomass varies. The model is also able to simulate priming of soil organic matter decomposition.

  16. Modeling marine surface microplastic transport to assess optimal removal locations

    OpenAIRE

    Sherman, P; Van Sebille, E

    2016-01-01

    Marine plastic pollution is an ever-increasing problem that demands immediate mitigation and reduction plans. Here, a model based on satellite-tracked buoy observations and scaled to a large data set of observations on microplastic from surface trawls was used to simulate the transport of plastics floating on the ocean surface from 2015 to 2025, with the goal to assess the optimal marine microplastic removal locations for two scenarios: removing the most surface microplastic and reducing the ...

  17. [Analysis on sustainable development of marine economy in Jiangsu Province based on marine ecological footprint correction model].

    Science.gov (United States)

    Yang, Shan; Wang, Yu-ting

    2011-03-01

    Based on the theories and methods of ecological footprint, the concept of marine ecological footprint was proposed. According to the characteristics of marine environment in Jiangsu Province, five sub-models of marine ecological footprints, including fishery, transporation, marine engineering construction, marine energy, and tidal flat, were constructed. The equilibrium factors of the five marine types were determined by using improved entropy method, and the marine footprints and capacities in Jiangsu Province from 2000 to 2008 were calculated and analyzed. In 2000-2008, the marine ecology footprint per capita in Jiangsu Province increased nearly seven times, from 36.90 hm2 to 252.94 hm2, and the ecological capacity per capita grew steadily, from 105.01 hm2 to 185.49 hm2. In 2000, the marine environment in the Province was in a state of ecological surplus, and the marine economy was in a weak sustainable development state. Since 2004, the marine ecological environment deteriorated sharply, with ecological deficit up to 109660.5 hm2, and the sustainability of marine economy declined. The high ecological footprint of fishery was the main reason for the ecological deficit. Tidal flat was the important reserve resource for the sustainable development of marine economy in Jiangsu Province.

  18. In situ trace metal analysis of Neoarchaean--Ordovician shallow-marine microbial-carbonate-hosted pyrites.

    Science.gov (United States)

    Gallagher, M; Turner, E C; Kamber, B S

    2015-07-01

    Pre-Cambrian atmospheric and oceanic redox evolutions are expressed in the inventory of redox-sensitive trace metals in marine sedimentary rocks. Most of the currently available information was derived from deep-water sedimentary rocks (black shale/banded iron formation). Many of the studied trace metals (e.g. Mo, U, Ni and Co) are sensitive to the composition of the exposed land surface and prevailing weathering style, and their oceanic inventory ultimately depends on the terrestrial flux. The validity of claims for increased/decreased terrestrial fluxes has remained untested as far as the shallow-marine environment is concerned. Here, the first systematic study of trace metal inventories of the shallow-marine environment by analysis of microbial carbonate-hosted pyrite, from ca. 2.65-0.52 Ga, is presented. A petrographic survey revealed a first-order difference in preservation of early diagenetic pyrite. Microbial carbonates formed before the 2.4 Ga great oxygenation event (GOE) are much richer in pyrite and contain pyrite grains of greater morphological variability but lesser chemical substitution than samples deposited after the GOE. This disparity in pyrite abundance and morphology is mirrored by the qualitative degree of preservation of organic matter (largely as kerogen). Thus, it seems that in microbial carbonates, pyrite formation and preservation were related to presence and preservation of organic C. Several redox-sensitive trace metals show interpretable temporal trends supporting earlier proposals derived from deep-water sedimentary rocks. Most notably, the shallow-water pyrite confirms a rise in the oceanic Mo inventory across the pre-Cambrian-Cambrian boundary, implying the establishment of efficient deep-ocean ventilation. The carbonate-hosted pyrite also confirms the Neoarchaean and early Palaeoproterozoic ocean had higher Ni concentration, which can now more firmly be attributed to a greater proportion of magnesian volcanic rock on land rather

  19. Marine Vessel Models in Changing Operational Conditions - A Tutorial

    DEFF Research Database (Denmark)

    Perez, Tristan; Sørensen, Asgeir; Blanke, Mogens

    2006-01-01

    conditions (VOC). However, since marine systems operate in changing VOCs, there is a need to adapt the models. To date, there is no theory available to describe a general model valid across different VOCs due to the complexity of the hydrodynamic involved. It is believed that system identification could......This tutorial paper provides an introduction, from a systems perspective, to the topic of ship motion dynamics of surface ships. It presents a classification of parametric models currently used for monitoring and control of marine vessels. These models are valid for certain vessel operational...... provide a significant contribution towards obtaining such a general model. Therefore, the main aim of the paper is to highlight the essential characteristics of marine system dynamics so as to provide a background for practitioners who would attempt future application of system identification techniques...

  20. Modeling Approaches for Describing Microbial Population Heterogeneity

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita

    in a computational (CFD) fluid dynamic model. The anaerobic Growth of a budding yeast population in a continuously run microbioreactor was used as example. The proposed integrated model describes the fluid flow, the local cell size and cell cycle position distributions, as well as the local concentrations of glucose...

  1. Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis

    Directory of Open Access Journals (Sweden)

    Marianna eTaffi

    2014-09-01

    Full Text Available The pressure to search effective bioremediation methodologies for contaminated ecosystems has led to the large-scale identification of microbial species and metabolic degradation pathways. However, minor attention has been paid to the study of bioremediation in marine food webs and to the definition of integrated strategies for reducing bioaccumulation in species. We propose a novel computational framework for analysing the multiscale effects of bioremediation at the ecosystem level, based on coupling food web bioaccumulation models and metabolic models of degrading bacteria. The combination of techniques from synthetic biology and ecological network analysis allows the specification of arbitrary scenarios of contaminant removal and the evaluation of strategies based on natural or synthetic microbial strains.In this study, we derive a bioaccumulation model of polychlorinated biphenyls (PCBs in the Adriatic food web, and we extend a metabolic reconstruction of Pseudomonas putida KT2440 (iJN746 with the aerobic pathway of PCBs degradation. We assess the effectiveness of different bioremediation scenarios in reducing PCBs concentration in species and we study indices of species centrality to measure their importance in the contaminant diffusion via feeding links.The analysis of the Adriatic sea case study suggests that our framework could represent a practical tool in the design of effective remediation strategies, providing at the same time insights into the ecological role of microbial communities within food webs.

  2. Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis.

    Science.gov (United States)

    Taffi, Marianna; Paoletti, Nicola; Angione, Claudio; Pucciarelli, Sandra; Marini, Mauro; Liò, Pietro

    2014-01-01

    The pressure to search effective bioremediation methodologies for contaminated ecosystems has led to the large-scale identification of microbial species and metabolic degradation pathways. However, minor attention has been paid to the study of bioremediation in marine food webs and to the definition of integrated strategies for reducing bioaccumulation in species. We propose a novel computational framework for analysing the multiscale effects of bioremediation at the ecosystem level, based on coupling food web bioaccumulation models and metabolic models of degrading bacteria. The combination of techniques from synthetic biology and ecological network analysis allows the specification of arbitrary scenarios of contaminant removal and the evaluation of strategies based on natural or synthetic microbial strains. In this study, we derive a bioaccumulation model of polychlorinated biphenyls (PCBs) in the Adriatic food web, and we extend a metabolic reconstruction of Pseudomonas putida KT2440 (iJN746) with the aerobic pathway of PCBs degradation. We assess the effectiveness of different bioremediation scenarios in reducing PCBs concentration in species and we study indices of species centrality to measure their importance in the contaminant diffusion via feeding links. The analysis of the Adriatic sea case study suggests that our framework could represent a practical tool in the design of effective remediation strategies, providing at the same time insights into the ecological role of microbial communities within food webs.

  3. A regional high resolution model of the marine mercury cycle.

    Science.gov (United States)

    Bieser, J.; Daewel, U.; Schrum, C.

    2017-12-01

    One of the main sources for mercury intoxication is the uptake of methylmercury from sea food. However, only little is known about the dynamics of methylmercury in the marine environment and its accumulation along the food chain. To further our understanding of the pathways from anthropogenic emissions of elemental mercury to the bio-accumulation of methylmercury in fish we developed the first regional Eulerian three dimensional multi-media chemistry transport model (MECOSMO) that includes atmosphere, ocean, and ecosystem. The marine part of the model includes a complete representation of the marine ecosystem ranging from phytoplankton up to higher trophic levels, including fish. We used the MECOSMO model to reconstruct mercury concentrations in water and biota in the North- and Baltic Sea for the past 60 years. Based on our model we examined the natural short and longterm variability of the system as well as long term trends in the distribution and amount of methylmercury in water and fish. Based on our findings we show how models can be utilized to develop future measurement strategies for marine mercury. Finally, the presented modelling system can be used to project the impact of future perturbations in the system (i.e.: emission reductions, climate change, nutrient control) on the mercury accumulation in sea food. Thereby, supporting the implementation of the Minamata Convention on Mercury on a regional scale by enabling us to estimate the impact of emission reductions on the marine mercury cycle.

  4. Marine Microbial Mats and the Search for Evidence of Life in Deep Time and Space

    Science.gov (United States)

    Des Marais, David J.

    2011-01-01

    Cyanobacterial mats in extensive seawater evaporation ponds at Guerrero Negro, Baja California, Mexico, have been excellent subjects for microbial ecology research. The studies reviewed here have documented the steep and rapidly changing environmental gradients experienced by mat microorganisms and the very high rates of biogeochemical processes that they maintained. Recent genetic studies have revealed an enormous diversity of bacteria as well as the spatial distribution of Bacteria, Archaea and Eukarya. These findings, together with emerging insights into the intimate interactions between these diverse populations, have contributed substantially to our understanding of the origins, environmental impacts, and biosignatures of photosynthetic microbial mats. The biosignatures (preservable cells, sedimentary fabrics, organic compounds, minerals, stable isotope patterns, etc.) potentially can serve as indicators of past life on early Earth. They also can inform our search for evidence of any life on Mars. Mars exploration has revealed evidence of evaporite deposits and thermal spring deposits; similar deposits on Earth once hosted ancient microbial mat ecosystems.

  5. Metabolic modeling of a mutualistic microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea; Pinel, Nicolas; Lie, Thomas J.; Leigh, John A.; Stahl, David A.

    2007-03-13

    The rate of production of methane in many environmentsdepends upon mutualistic interactions between sulfate-reducing bacteriaand methanogens. To enhance our understanding of these relationships, wetook advantage of the fully sequenced genomes of Desulfovibrio vulgarisand Methanococcus maripaludis to produce and analyze the firstmultispecies stoichiometric metabolic model. Model results were comparedto data on growth of the co-culture on lactate in the absence of sulfate.The model accurately predicted several ecologically relevantcharacteristics, including the flux of metabolites and the ratio of D.vulgaris to M. maripaludis cells during growth. In addition, the modeland our data suggested that it was possible to eliminate formate as aninterspecies electron shuttle, but hydrogen transfer was essential forsyntrophic growth. Our work demonstrated that reconstructed metabolicnetworks and stoichiometric models can serve not only to predictmetabolic fluxes and growth phenotypes of single organisms, but also tocapture growth parameters and community composition of simple bacterialcommunities.

  6. Pore-Scale Model for Microbial Growth

    Science.gov (United States)

    Tartakovsky, G.; Tartakovsky, A. M.; Scheibe, T. D.

    2011-12-01

    A lagrangian particle model based on smoothed particle hydrodynamics (SPH) is used to simulate pore-scale flow, reactive transport and biomass growth which is controlled by the mixing of an electron donor and acceptor, in a microfluidic porous cell. The experimental results described in Ch. Zhang et al "Effects of pore-scale heterogeneity and transverse mixing on bacterial growth in porous media" were used for this study. The model represents the homogeneous pore structure of a uniform array of cylindrical posts with microbes uniformly distributed on the grain surfaces. Each one of the two solutes (electron donor and electron acceptor) enters the domain unmixed through separate inlets. In the model, pair-wise particle-particle interactions are used to simulate interactions within the biomass, and both biomass-fluid and biomass-soil grain interactions. The biomass growth rate is described by double Monod kinetics. For the set of parameters used in the simulations the model predicts that: 1) biomass grows in the shape of bridges connecting soil grains and oriented in the direction of flow so as to minimize resistance to the fluid flow; and 2) the biomass growth occurs only in the mixing zone. Using parameters available in the literature, the biomass growth model agrees qualitatively with the experimental results. In order to achieve quantitative agreement, model calibration is required.

  7. A Biogeotechnical approach to Stabilize Soft Marine Soil with a Microbial Organic Material called Biopolymer

    Science.gov (United States)

    Chang, I.; Cho, G. C.; Kwon, Y. M.; Im, J.

    2017-12-01

    The importance and demands of offshore and coastal area development are increasing due to shortage of usable land and to have access to valuable marine resources. However, most coastal soils are soft sediments, mainly composed with fines (silt and clay) and having high water and organic contents, which induce complicated mechanical- and geochemical- behaviors and even be insufficient in Geotechnical engineering aspects. At least, soil stabilization procedures are required for those soft sediments, regardless of the purpose of usage on the site. One of the most common soft soil stabilization method is using ordinary cement as a soil strengthening binder. However, the use of cement in marine environments is reported to occur environmental concerns such as pH increase and accompanying marine ecosystem disturbance. Therefore, a new environmentally-friendly treatment material for coastal and offshore soils. In this study, a biopolymer material produced by microbes is introduced to enhance the physical behavior of a soft tidal flat sediment by considering the biopolymer rheology, soil mineralogy, and chemical properties of marine water. Biopolymer material used in this study forms inter-particle bonds between particles which is promoted through cation-bridges where the cations are provided from marine water. Moreover, biopolymer treatment renders unique stress-strain relationship of soft soils. The mechanical stiffness (M) instantly increase with the presence of biopolymer, while time-dependent settlement behavior (consolidation) shows a big delay due to the viscous biopolymer hydrogels in pore spaces.

  8. Optimisation of Marine Boilers using Model-based Multivariable Control

    DEFF Research Database (Denmark)

    Solberg, Brian

    Traditionally, marine boilers have been controlled using classical single loop controllers. To optimise marine boiler performance, reduce new installation time and minimise the physical dimensions of these large steel constructions, a more comprehensive and coherent control strategy is needed....... This research deals with the application of advanced control to a specific class of marine boilers combining well-known design methods for multivariable systems. This thesis presents contributions for modelling and control of the one-pass smoke tube marine boilers as well as for hybrid systems control. Much...... of the focus has been directed towards water level control which is complicated by the nature of the disturbances acting on the system as well as by low frequency sensor noise. This focus was motivated by an estimated large potential to minimise the boiler geometry by reducing water level fluctuations...

  9. Review and perspective on mathematical modeling of microbial ecosystems.

    Science.gov (United States)

    Succurro, Antonella; Ebenhöh, Oliver

    2018-03-14

    Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?' An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction. © 2018 The Author(s).

  10. Elevated temperature alters carbon cycling in a model microbial community

    Science.gov (United States)

    Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

    2013-12-01

    Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

  11. Presence and effects of marine microbial biofilms on biocide-based antifouling paints

    DEFF Research Database (Denmark)

    Yebra, Diego Meseguer; Kiil, Søren; Erik Weinell, Claus

    2006-01-01

    Marine microorganisms are capable of successfully colonizing toxic surfaces through the formation of biofilm structures. In this article, most of the literature reporting the presence of marine biofilms on chemically-active antifouling paints is briefly reviewed. Of special concern is the influence...... of the dense extracellular polymeric substances (EPS) matrix on the release rate of the compounds involved in antifouling paint performance (i.e. active compounds and controlled-release binder molecules). A deeper understanding of these phenomena is of interest for both environmental legislators and paint...

  12. Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes

    Directory of Open Access Journals (Sweden)

    Shiue-Lin eLi

    2015-02-01

    Full Text Available Sulfide is a common product of marine anaerobic respiration, and a potent reactant biologically and geochemically. Here we demonstrate the impact on microbial communities with the removal of sulfide via electrochemical methods. The use of differential pulse voltammetry revealed that the oxidation of soluble sulfide was seen at + mV (vs. SHE at all pH ranges tested (from pH = 4 to 8, while non-ionized sulfide, which dominated at pH = 4 was poorly oxidized via this process. Two mixed cultures (CAT and LA were enriched from two different marine sediments (from Catalina Island, CAT; from the Port of Los Angeles, LA in serum bottles using a seawater medium supplemented with lactate, sulfate, and yeast extract, to obtain abundant biomass. Both CAT and LA cultures were inoculated in electrochemical cells (using yeast-extract-free seawater medium as an electrolyte equipped with carbon-felt electrodes. In both cases, when potentials of +630 or 130 mV (vs. SHE were applied, currents were consistently higher at +630 then at 0 mV, indicating more sulfide being oxidized at the higher potential. In addition, higher organic-acid and sulfate conversion rates were found at +630 mV with CAT, while no significant differences were found with LA at different potentials. The results of microbial-community analyses revealed a decrease in diversity for both CAT and LA after electrochemical incubation. In addition, some bacteria (e.g., Clostridium and Arcobacter not well known to be capable of extracellular electron transfer, were found to be dominant in the electrochemical cells. Thus, even though the different mixed cultures have different tolerances for sulfide, electrochemical-sulfide removal can lead to major population changes.

  13. Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro in Okinawa Island, Japan

    Directory of Open Access Journals (Sweden)

    Taha Soliman

    2017-12-01

    Full Text Available Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan “Kaichu-Doro” Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10 from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60–80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.

  14. Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.

    Science.gov (United States)

    Soliman, Taha; Reimer, James D; Yang, Sung-Yin; Villar-Briones, Alejandro; Roy, Michael C; Jenke-Kodama, Holger

    2017-01-01

    Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan "Kaichu-Doro" Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores ( n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m) than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60-80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.

  15. Factors affecting virus dynamics and microbial host-virus interactions in marine environments

    NARCIS (Netherlands)

    Mojica, K.D.A.; Brussaard, C.P.D.

    2014-01-01

    Marine microorganisms constitute the largest percentage of living biomass and serve as the major driving force behind nutrient and energy cycles. While viruses only comprise a small percentage of this biomass (i.e., 5%), they dominate in numerical abundance and genetic diversity. Through host

  16. Microbially mediated carbonation of marine alkaline minerals : Potential for concrete crack healing

    NARCIS (Netherlands)

    Jonkers, H.M.; Palin, D.; Flink, P.J.; Thijssen, A.

    2013-01-01

    Concrete constructions in the marine environment suffer from chemical attack of sea salts which can induce damage to both the concrete matrix and embedded steel reinforcement. For example, ingress of sulfate and chloride ions can respectively result in detrimental ettringite formation and enhanced

  17. Development of a Fuzzy Model for Iranian Marine Casualties Management

    Directory of Open Access Journals (Sweden)

    Ali Moradi

    2014-09-01

    Full Text Available Marine Accident investigation multidimensional and complex, so this study aimed to provide a systematic approach to determining the degree of the most influential parameters (dimensions in accident occurrence in order to improve marine safety in the direction of good governance. In this paper, two-phase procedures are proposed. The first stage utilizes the fuzzy Delphi method (FDM to determine the critical factors of Marine Accident Investigation by interviewing the pertinent authorities. In the second stage, the fuzzy analytic hierarchy process (FAHP is applied to pair fuzzy numbers as measurable indices and finally to rank by degree each influential criterion within accident investigation. This study considers 1 goal, 4 aspects, and 31 criteria (parameters and establishes a ranking model that allows decision-makers to assess the prior ordering of reasons and sort by the most effective parameters involved in marine accident occurrence. The empirical study indicated that People, working and living conditions, effect is considered the highest ranking aspect, and Ability, skills, and knowledge of workers is considered the most important evaluation criterion overall by experts. These results were derived from fuzzy Delphi analytical hierarchy processing (FDAHP. A demonstration of the prior ordering of accident-causing parameters by authorities was addressed as well. Therefore, ranking the priority of every influential criterion (parameter will help marine transportation decision makers emphasize the areas in which to improve in order to prevent future marine accidents.

  18. Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems.

    Science.gov (United States)

    Li, Xiang; Harwood, Valerie J; Nayak, Bina; Weidhaas, Jennifer L

    2016-01-04

    Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  19. Analysis of Neurotoxic Amino Acids from Marine Waters, Microbial Mats, and Seafood Destined for Human Consumption in the Arabian Gulf.

    Science.gov (United States)

    Chatziefthimiou, Aspassia D; Deitch, Eric J; Glover, William B; Powell, James T; Banack, Sandra Anne; Richer, Renee A; Cox, Paul A; Metcalf, James S

    2018-01-01

    Human health risks associated with exposure to algal and cyanobacterial toxins (phycotoxins) have been largely concerned with aquatic habitats. People inhabiting desert environments may be exposed to phycotoxins present in terrestrial environments, where cyanobacterial crusts dominate. Seafood comprises a significant portion of the human diet in desert environments proximal to an ocean or sea. Consequently, in addition to terrestrial exposure to cyanotoxins, the potential exists that seafood may be an important exposure route for cyanotoxins in desert regions. Understanding the possible risk of exposure from seafood will help create cyanotoxin health guidelines for people living in environments that rely on seafood. Commonly-consumed local seafood products destined for human consumption were purchased from a fish market in Doha, Qatar. Organs were excised, extracted, and analyzed for the neurotoxic amino acid β-N-methylamino-L-alanine (BMAA) and the isomers 2,4-diaminobutyric acid (DAB) and N-2(aminoethyl)glycine (AEG). The presence and concentration of neurotoxic amino acids were investigated in organisms from various trophic levels to examine the potential for biomagnification. Although BMAA and isomers were detected in marine microbial mats, as well as in marine plankton net trawls associated with diatoms and dinoflagellates, in seafood, only AEG and DAB were present at low concentrations in various trophic levels. The findings of this study suggest that exposure to neurotoxic amino acids through seafood in the Arabian Gulf may be minor, yet the presence of BMAA in phytoplankton confirms the need for further monitoring of marine waters and seafood to protect human health.

  20. Marine Corps Maneuver Squad Leader Mastery Model

    Science.gov (United States)

    2012-12-17

    developed a set of five competencies (sensemaking, adaptability, problem solving,  metacognition , and attentional control) and ten enabling cognitive and... metacognition ,  and  attentional  control)  and  the  ten  CARS  (cognitive  flexibility,  resilience,  anomaly  detection, change detection...communication and training to  each individual.        Takes on more of a  mentorship role and not just  a  teacher . Helps Marines  understand the

  1. Experimental Constraints on Microbial Liberation of Structural Iron from Common Clay Minerals in Marine Sediments

    Science.gov (United States)

    Metcalfe, K. S.; Gaines, R. R.; Trang, J.; Scott, S. W.; Crane, E. J.; Lackey, J.; Prokopenko, M. G.; Berelson, W.

    2013-12-01

    Iron is a limiting nutrient in many marine settings. The marine Fe-cycle is complex because Fe may be used as an electron donor or acceptor and cycled many times before ultimate burial in sediments. Thus, the availability of iron plays a large role in the marine carbon cycle, influencing not only the extent of primary productivity but also the oxidation of organic matter in sediments. The primary constituents of marine sediments are clay minerals, which commonly contain lattice-bound Fe in octahedral sites. In marine settings, the pool of Fe bound within silicate mineral lattices has long been considered reactive only over long timescales, and thus non-bioavailable. In vitro experimental evidence has shown that lab cultures of Fe-reducing bacteria are able to utilize structurally-bound Fe (III) from the crystal lattice of nontronite, an uncommon but particularly Fe-rich (> 12 wt.%) smectite. Importantly, this process is capable of liberating Fe (II) to solution, where it is available to biotic processes as an electron donor. In order to constrain the capacity of naturally-occurring marine bacteria to liberate structurally-coordinated Fe from the lattices of common clay minerals, we exposed a suite of 16 different clay minerals (0.8-13.9 wt.% Fe) to lab cultures of known Fe-reducer S. onenidensis MR-1 and to a natural consortium of Fe-reducing microbes from the San Pedro and Santa Monica Basins over timescales ranging from 7-120 days. Clay minerals were treated with Na-dithionite to extract surface-bound Fe prior to exposure. Crystallographic data and direct measurements of Fe in solution demonstrate the release of structural Fe from all clay minerals analyzed. Neoformation of illite and amorphous quartz were observed. The array of clay minerals and microbes used in this experiment complement past findings and suggest that common clay minerals may represent a large and previously unrecognized pool of bioavailable Fe in the world ocean that contributes significantly

  2. In-Drift Microbial Communities Model Validation Calculations

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Jolley

    2001-09-24

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  3. In-Drift Microbial Communities Model Validation Calculation

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Jolley

    2001-10-31

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  4. In-Drift Microbial Communities Model Validation Calculations

    International Nuclear Information System (INIS)

    Jolley, D.M.

    2001-01-01

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS MandO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS MandO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS MandO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS MandO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data

  5. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    D.M. Jolley

    2001-12-18

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data.

  6. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    International Nuclear Information System (INIS)

    D.M. Jolley

    2001-01-01

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M andO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M andO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M andO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M andO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data

  7. Integrating microbial physiology and enzyme traits in the quality model

    Science.gov (United States)

    Sainte-Marie, Julien; Barrandon, Matthieu; Martin, Francis; Saint-André, Laurent; Derrien, Delphine

    2017-04-01

    Microbe activity plays an undisputable role in soil carbon storage and there have been many calls to integrate microbial ecology in soil carbon (C) models. With regard to this challenge, a few trait-based microbial models of C dynamics have emerged during the past decade. They parameterize specific traits related to decomposer physiology (substrate use efficiency, growth and mortality rates...) and enzyme properties (enzyme production rate, catalytic properties of enzymes…). But these models are built on the premise that organic matter (OM) can be represented as one single entity or are divided into a few pools, while organic matter exists as a continuum of many different compounds spanning from intact plant molecules to highly oxidised microbial metabolites. In addition, a given molecule may also exist in different forms, depending on its stage of polymerization or on its interactions with other organic compounds or mineral phases of the soil. Here we develop a general theoretical model relating the evolution of soil organic matter, as a continuum of progressively decomposing compounds, with decomposer activity and enzyme traits. The model is based on the notion of quality developed by Agren and Bosatta (1998), which is a measure of molecule accessibility to degradation. The model integrates three major processes: OM depolymerisation by enzyme action, OM assimilation and OM biotransformation. For any enzyme, the model reports the quality range where this enzyme selectively operates and how the initial quality distribution of the OM subset evolves into another distribution of qualities under the enzyme action. The model also defines the quality range where the OM can be uptaken and assimilated by microbes. It finally describes how the quality of the assimilated molecules is transformed into another quality distribution, corresponding to the decomposer metabolites signature. Upon decomposer death, these metabolites return to the substrate. We explore here the how

  8. A GPU Reaction Diffusion Soil-Microbial Model

    Science.gov (United States)

    Falconer, Ruth; Houston, Alasdair; Schmidt, Sonja; Otten, Wilfred

    2014-05-01

    Parallelised algorithms are frequent in bioinformatics as a consequence of the close link to informatics - however in the field of soil science and ecology they are less prevalent. A current challenge in soil ecology is to link habitat structure to microbial dynamics. Soil science is therefore entering the 'big data' paradigm as a consequence of integrating data pertinent to the physical soil environment obtained via imaging and theoretical models describing growth and development of microbial dynamics permitting accurate analyses of spatio-temporal properties of different soil microenvironments. The microenvironment is often captured by 3D imaging (CT tomography) which yields large datasets and when used in computational studies the physical sizes of the samples that are amenable to computation are less than 1 cm3. Today's commodity graphics cards are programmable and possess a data parallel architecture that in many cases is capable of out-performing the CPU in terms of computational rates. The programmable aspect is achieved via a low-level parallel programming language (CUDA, OpenCL and DirectX). We ported a Soil-Microbial Model onto the GPU using the DirectX Compute API. We noted a significant computational speed up as well as an increase in the physical size that can be simulated. Some of the drawbacks of such an approach were concerned with numerical precision and the steep learning curve associated with GPGPU technologies.

  9. Interactions between marine snow and heterotrophic bacteria: aggregate formation and microbial dynamics

    DEFF Research Database (Denmark)

    Grossart, H.P.; Kiørboe, Thomas; Tang, K.W.

    2006-01-01

    as well as abundance, colonization behaviour, and community composition of bacteria during the growth of 2 marine diatoms (Thalassiosira weissflogii and Navicula sp.) under axenic and non-axenic conditions. Community composition of free-living and attached bacteria during phytoplankton growth...... bacteria depended on phytoplankton growth and aggregation dynamics. The community composition of especially attached bacteria significantly differed between the 2 algal cultures. Our study suggests that phytoplankton aggregation and vertical fluxes are closely linked to interactions between the marine...... and aggregation was studied by amplification of 16S rRNA gene fragments and denaturing gradient gel electrophoresis (DGGE). Our results show that the presence of bacteria was a prerequisite for aggregation of T. weissflogii but not of Navicula sp. Occurrences of distinct populations of free-living and attached...

  10. Habitat modelling predictions highlight seasonal relevance of Marine Protected Areas for marine megafauna

    Science.gov (United States)

    Lambert, C.; Virgili, A.; Pettex, E.; Delavenne, J.; Toison, V.; Blanck, A.; Ridoux, V.

    2017-07-01

    According to the European Union Habitats and Birds Directives, EU Member States must extend the Natura 2000 network to marine ecosystems, through the designation of Marine Protected Areas (MPAs). However, the initial status of cetacean and seabird communities across European waters is often poorly understood. It is assumed that an MPA is justified where at least 1% of the "national population" of a species is present during at least part of its biological cycle. The aim of the present work was to use model-based cetacean and seabird distribution to assess the networks of existing Natura 2000 sites and offshore proposed areas of biological interest. The habitat models used here were Generalised Additive Models computed from aerial surveys observational data collected during the winter 2011-2012 and the summer 2012 across the English Channel, Bay of Biscay and north-western Mediterranean Sea. Based on these models, a ratio between species relative abundance predicted within each MPA and the total relative abundance predicted over the French Atlantic or Mediterranean marine regions was computed and compared to the 1% threshold. This assessment was conducted for winter and summer independently, providing information for assessing the relevance of individual MPAs and MPA networks at a seasonal scale. Our results showed that the existing network designed for coastal seabird species was relevant in both marine regions. In contrast, a clear shortfall was identified for offshore seabird species in the Atlantic region and for cetaceans in both regions. Moreover, the size of MPAs appeared to be a crucial feature, with larger MPAs being relevant for more species. Finally, we showed that the proposed large offshore areas of interest would constitute a highly relevant network for all offshore species, with e.g. up to 61% of the Globicephalinae population in the Atlantic French waters being present within these areas.

  11. A theoretical microbial contamination model for a human Mars mission

    Science.gov (United States)

    Lupisella, Mark Lewis

    Contamination from a human presence on Mars could significantly compromise the search for extraterrestrial life. In particular, the difficulties in controlling microbial contamination, the potential for terrestrial microbes to grow, evolve, compete, and modify the Martian environment, and the likely microbial nature of putative Martian life, make microbial contamination worthy of focus as we begin to plan for a human mission to Mars. This dissertation describes a relatively simple theoretical model that can be used to explore how microbial contamination from a human Mars mission might survive and grow in the Martian soil environment surrounding a habitat. A user interface has been developed to allow a general practitioner to choose values and functions for almost all parameters ranging from the number of astronauts to the half-saturation constants for microbial growth. Systematic deviations from a baseline set of parameter values are explored as potential plausible scenarios for the first human Mars missions. The total viable population and population density are the primary state variables of interest, but other variables such as the total number of births and total dead and viable microbes are also tracked. The general approach was to find the most plausible parameter value combinations that produced a population density of 1 microbe/cm3 or greater, a threshold that was used to categorize the more noteworthy populations for subsequent analysis. Preliminary assessments indicate that terrestrial microbial contamination resulting from leakage from a limited human mission (perhaps lasting up to 5 months) will not likely become a problematic population in the near-term as long as reasonable contamination control measures are implemented (for example, a habitat leak rate no greater than 1% per hour). However, there appear to be plausible, albeit unlikely, scenarios that could cause problematic populations, depending in part on (a) the initial survival fraction and

  12. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing.

    Science.gov (United States)

    Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

    2011-09-01

    Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species--the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E-9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E-14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356-896 OTUs) was >2-fold higher than in the MI (112-567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that

  13. Integrating microbial physiology and physio-chemical principles in soils with the MIcrobial-MIneral Carbon Stabilization (MIMICS) model

    Science.gov (United States)

    Wieder, W. R.; Grandy, A. S.; Kallenbach, C. M.; Bonan, G. B.

    2014-07-01

    A growing body of literature documents the pressing need to develop soil biogeochemistry models that more accurately reflect contemporary understanding of soil processes and better capture soil carbon (C) responses to environmental perturbations. Models that explicitly represent microbial activity offer inroads to improve representations of soil biogeochemical processes, but have yet to consider relationships between litter quality, functional differences in microbial physiology, and the physical protection of microbial byproducts in forming stable soil organic matter (SOM). To address these limitations, we introduce the MIcrobial-MIneral Carbon Stabilization (MIMICS) model, and evaluate it by comparing site-level soil C projections with observations from a long-term litter decomposition study and soil warming experiment. In MIMICS, the turnover of litter and SOM pools is governed by temperature-sensitive Michaelis-Menten kinetics and the activity of two physiologically distinct microbial functional types. The production of microbial residues through microbial turnover provides inputs to SOM pools that are considered physically or chemically protected. Soil clay content determines the physical protection of SOM in different soil environments. MIMICS adequately simulates the mean rate of leaf litter decomposition observed at temperate and boreal forest sites, and captures observed effects of litter quality on decomposition rates. Moreover, MIMICS better captures the response of SOM pools to experimental warming, with rapid SOM losses but declining temperature sensitivity to long-term warming, compared with a more conventional model structure. MIMICS incorporates current microbial theory to explore the mechanisms by which litter C is converted to stable SOM, and to improve predictions of soil C responses to environmental change.

  14. Modeling marine surface microplastic transport to assess optimal removal locations

    NARCIS (Netherlands)

    Sherman, Peter; Van Sebille, Erik

    2016-01-01

    Marine plastic pollution is an ever-increasing problem that demands immediate mitigation and reduction plans. Here, a model based on satellite-tracked buoy observations and scaled to a large data set of observations on microplastic from surface trawls was used to simulate the transport of plastics

  15. Enrichment of the hydrogen-producing microbial community from marine intertidal sludge by different pretreatment methods

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hongyan [Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Shinan District, Qingdao 266071, Shandong (China); College of Marine Science and Engineering, University of Science and Technology, Tianjin 300457 (China); Graduate School, Chinese Academy of Sciences, Beijing 100039 (China); Wang, Guangce [Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Shinan District, Qingdao 266071, Shandong (China); College of Marine Science and Engineering, University of Science and Technology, Tianjin 300457 (China); Zhu, Daling; Pan, Guanghua [College of Marine Science and Engineering, University of Science and Technology, Tianjin 300457 (China)

    2009-12-15

    To determine the effects of pretreatment on hydrogen production and the hydrogen-producing microbial community, we treated the sludge from the intertidal zone of a bathing beach in Tianjin with four different pretreatment methods, including acid treatment, heat-shock, base treatment as well as freezing and thawing. The results showed that acid pretreatment significantly promoted the hydrogen production by sludge and provided the highest efficiency of hydrogen production among the four methods. The efficiency of the hydrogen production of the acid-pretreated sludge was 0.86 {+-} 0.07 mol H{sub 2}/mol glucose (mean {+-} S.E.), whereas that of the sludge treated with heat-shock, freezing and thawing, base method and control was 0.41 {+-} 0.03 mol H{sub 2}/mol glucose, 0.17 {+-} 0.01 mol H{sub 2}/mol glucose, 0.11 {+-} 0.01 mol H{sub 2}/mol glucose and 0.20 {+-} 0.04 mol H{sub 2}/mol glucose, respectively. The result of denaturing gradient gel electrophoresis (DGGE) showed that pretreatment methods altered the composition of the microbial community that accounts for hydrogen production. Acid and heat pretreatments were favorable to enrich the dominant hydrogen-producing bacterium, i.e. Clostridium sp., Enterococcus sp. and Bacillus sp. However, besides hydrogen-producing bacteria, much non-hydrogen-producing Lactobacillus sp. was also found in the sludge pretreated with base, freezing and thawing methods. Therefore, based on our results, we concluded that, among the four pretreatment methods using acid, heat-shock, base or freezing and thawing, acid pretreatment was the most effective method for promoting hydrogen production of microbial community. (author)

  16. Apatite and Chitin Amendments Promote Microbial Activity and Augment Metal Removal in Marine Sediments

    Science.gov (United States)

    2013-07-01

    10.1111/j.1574-6941.2006.00203.x [43] G. Garau, P. Castaldi, L. Santona, P. Deiana and P. Melis, “Influence of Red Mud , Zeolite and Lime on Heavy Metal...Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 J. KAN ET AL. 52 metal recycling facility to remediate high Zn levels in nearby...ppm, and Zn and Cr = 1.0 ppm. 2.3.1. Microbiological Analysis Microbial biomass was determined by epifluorescence microscopy. DNA extraction , PCR

  17. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    International Nuclear Information System (INIS)

    Wang, Yifeng; Papenguth, Hans W.

    2000-01-01

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

  18. Modeling Marine Electromagnetic Survey with Radial Basis Function Networks

    Directory of Open Access Journals (Sweden)

    Agus Arif

    2014-11-01

    Full Text Available A marine electromagnetic survey is an engineering endeavour to discover the location and dimension of a hydrocarbon layer under an ocean floor. In this kind of survey, an array of electric and magnetic receivers are located on the sea floor and record the scattered, refracted and reflected electromagnetic wave, which has been transmitted by an electric dipole antenna towed by a vessel. The data recorded in receivers must be processed and further analysed to estimate the hydrocarbon location and dimension. To conduct those analyses successfuly, a radial basis function (RBF network could be employed to become a forward model of the input-output relationship of the data from a marine electromagnetic survey. This type of neural networks is working based on distances between its inputs and predetermined centres of some basis functions. A previous research had been conducted to model the same marine electromagnetic survey using another type of neural networks, which is a multi layer perceptron (MLP network. By comparing their validation and training performances (mean-squared errors and correlation coefficients, it is concluded that, in this case, the MLP network is comparatively better than the RBF network[1].[1] This manuscript is an extended version of our previous paper, entitled Radial Basis Function Networks for Modeling Marine Electromagnetic Survey, which had been presented on 2011 International Conference on Electrical Engineering and Informatics, 17-19 July 2011, Bandung, Indonesia.

  19. Commercial product exploitation from marine microbial biodiversity: some legal and IP issues.

    Science.gov (United States)

    Tichet, Camille; Nguyen, Hong Khanh; Yaakoubi, Sefia El; Bloch, Jean-François

    2010-09-01

    The biodiversity found in the marine environment is remarkable and yet largely unknown compared with the terrestrial one. The associated genetic resource, also wide and unrevealed, has raised a strong interest from the scientific and industrial community. However, despite this growing interest, the discovery of new compounds extracted from marine organisms, more precisely from microorganisms, is ruled by a complex legislation. The access and transfer of genetic resource are ruled by the Convention on Biological Diversity. One of the three core objectives of this convention is to ensure the fair and equitable sharing of benefits generated by the use of genetic resources and to split these benefits between the different stakeholders. From the discovery of a microorganism to the commercialization of a product, three main stakeholders are involved: providers of microorganisms, e.g. academic institutes, the scientists who will perform R&D on biodiversity, and the industrial companies which will commercialize the final product arising from the R&D results. This article describes how difficult and complex it might be to ensure a fair distribution of benefits of this research between the parties. © 2010 The Authors; Journal compilation © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

  20. A grounded theory model for analysis of marine accidents.

    Science.gov (United States)

    Mullai, Arben; Paulsson, Ulf

    2011-07-01

    The purpose of this paper was to design a conceptual model for analysis of marine accidents. The model is grounded on large amounts of empirical data, i.e. the Swedish Maritime Administration database, which was thoroughly studied. This database contains marine accidents organized by ship and variable. The majority of variables are non-metric and some have never been analyzed because of the large number of values. Summary statistics were employed in the data analysis. In order to develop a conceptual model, the database variables were clustered into eleven main categories or constructs, which were organized according to their properties and connected with the path diagram of relationships. For demonstration purposes, one non-metric and five metric variables were selected, namely fatality, ship's properties (i.e. age, gross register tonnage, and length), number of people on board, and marine accidents. These were analyzed using the structural equation modeling (SEM) approach. The combined prediction power of the 'ship's properties' and 'number of people on board' independent variables accounted for 65% of the variance of the fatality. The model development was largely based on the data contained in the Swedish database. However, as this database shares a number of variables in common with other databases in the region and the world, the model presented in this paper could be applied to other datasets. The model has both theoretical and practical values. Recommendations for improvements in the database are also suggested. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Optimal foraging in marine ecosystem models: selectivity, profitability and switching

    DEFF Research Database (Denmark)

    Visser, Andre W.; Fiksen, Ø.

    2013-01-01

    ecological mechanics and evolutionary logic as a solution to diet selection in ecosystem models. When a predator can consume a range of prey items it has to choose which foraging mode to use, which prey to ignore and which ones to pursue, and animals are known to be particularly skilled in adapting...... to the preference functions commonly used in models today. Indeed, depending on prey class resolution, optimal foraging can yield feeding rates that are considerably different from the ‘switching functions’ often applied in marine ecosystem models. Dietary inclusion is dictated by two optimality choices: 1...... by letting predators maximize energy intake or more properly, some measure of fitness where predation risk and cost are also included. An optimal foraging or fitness maximizing approach will give marine ecosystem models a sound principle to determine trophic interactions...

  2. Ocean acidification of a coastal Antarctic marine microbial community reveals a critical threshold for CO2 tolerance in phytoplankton productivity

    Science.gov (United States)

    Deppeler, Stacy; Petrou, Katherina; Schulz, Kai G.; Westwood, Karen; Pearce, Imojen; McKinlay, John; Davidson, Andrew

    2018-01-01

    High-latitude oceans are anticipated to be some of the first regions affected by ocean acidification. Despite this, the effect of ocean acidification on natural communities of Antarctic marine microbes is still not well understood. In this study we exposed an early spring, coastal marine microbial community in Prydz Bay to CO2 levels ranging from ambient (343 µatm) to 1641 µatm in six 650 L minicosms. Productivity assays were performed to identify whether a CO2 threshold existed that led to a change in primary productivity, bacterial productivity, and the accumulation of chlorophyll a (Chl a) and particulate organic matter (POM) in the minicosms. In addition, photophysiological measurements were performed to identify possible mechanisms driving changes in the phytoplankton community. A critical threshold for tolerance to ocean acidification was identified in the phytoplankton community between 953 and 1140 µatm. CO2 levels ≥ 1140 µatm negatively affected photosynthetic performance and Chl a-normalised primary productivity (csGPP14C), causing significant reductions in gross primary production (GPP14C), Chl a accumulation, nutrient uptake, and POM production. However, there was no effect of CO2 on C : N ratios. Over time, the phytoplankton community acclimated to high CO2 conditions, showing a down-regulation of carbon concentrating mechanisms (CCMs) and likely adjusting other intracellular processes. Bacterial abundance initially increased in CO2 treatments ≥ 953 µatm (days 3-5), yet gross bacterial production (GBP14C) remained unchanged and cell-specific bacterial productivity (csBP14C) was reduced. Towards the end of the experiment, GBP14C and csBP14C markedly increased across all treatments regardless of CO2 availability. This coincided with increased organic matter availability (POC and PON) combined with improved efficiency of carbon uptake. Changes in phytoplankton community production could have negative effects on the Antarctic food web and the

  3. Marine Aerosol Precursor Emissions for Earth System Models

    Energy Technology Data Exchange (ETDEWEB)

    Maltrud, Mathew Einar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-07-25

    Dimethyl sulfide (DMS) is generated by marine ecosystems and plays a major role in cloud formation over the ocean. Currently, Earth System Models use imposed flux of DMS from the ocean to the atmosphere that is independent of the climate state. We have added DMS as a prognostic variable to the Community Earth System Model (CESM) that depends on the distribution of phytoplankton species, and thus changes with climate.

  4. Outlook on marine propeller noise and cavitation modelling

    OpenAIRE

    Lidtke, Artur Konrad; Turnock, Stephen R.; Humphrey, Victor F.

    2014-01-01

    Two computational studies are presented in this paper. First, the Potsdam Propeller Test Case which is used to demonstrate the capabilities of mass transfer cavitation models, more precisely the model by Sauer and Schnerr, in tackling the problem of marine propeller cavitation. It is shown that the extents of the predicted cavitation regions agree well with the experiment but suffer from the fact that the tip vortices and the associated low pressure regions are under resolved when URANS is ut...

  5. Marine

    NARCIS (Netherlands)

    Govers, L.; Man in 't Veld, W.A.; Meffert, J.P.; Bouma, T.J.; van Rijswick, P.C.; Heusinkveld, J.H.T.; Orth, R.J.; van Katwijk, M.M.; van der Heide, T.

    2016-01-01

    Phytophthora species are potent pathogens that can devastate terrestrial plants, causing billions of dollars of damage yearly to agricultural crops and harming fragile ecosystems worldwide. Yet, virtually nothing is known about the distribution and pathogenicity of their marine relatives.

  6. Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

    Energy Technology Data Exchange (ETDEWEB)

    Hofmockel, Kirsten; Hobbie, Erik

    2017-07-31

    Our funded research focused on soil organic matter dynamics and plant-microbe interactions by examining the role of belowground processes and mechanisms across scales, including decomposition of organic molecules, microbial interactions, and plant-microbe interactions associated with a changing climate. Research foci included mycorrhizal mediated priming of soil carbon turnover, organic N use and depolymerization by free-living microbes and mycorrhizal fungi, and the use of isotopes as additional constraints for improved modeling of belowground processes. This work complemented the DOE’s mandate to understand both the consequences of atmospheric and climatic change for key ecosystems and the feedbacks on C cycling.

  7. Models for Microbial Fuel Cells: A critical review

    Science.gov (United States)

    Xia, Chengshuo; Zhang, Daxing; Pedrycz, Witold; Zhu, Yingmin; Guo, Yongxian

    2018-01-01

    Microbial fuel cells (MFCs) have been widely viewed as one of the most promising alternative sources of renewable energy. A recognition of needs of efficient development methods based on multidisciplinary research becomes crucial for the optimization of MFCs. Modeling of MFCs is an effective way for not only gaining a thorough understanding of the effects of operation conditions on the performance of power generation but also becomes of essential interest to the successful implementation of MFCs. The MFC models encompass the underlying reaction process and limiting factors of the MFC. The models come in various forms, such as the mathematical equations or the equivalent circuits. Different modeling focuses and approaches of the MFC have emerged. In this study, we present a state of the art of MFCs modeling; the past modeling methods are reviewed as well. Models and modeling methods are elaborated on based on the classification provided by Mechanism-based models and Application-based models. Mechanisms, advantages, drawbacks, and application fields of different models are illustrated as well. We exhibit a complete and comprehensive exposition of the different models for MFCs and offer further guidance to promote the performance of MFCs.

  8. Seasonal variability in the persistence of dissolved environmental DNA (eDNA in a marine system: The role of microbial nutrient limitation.

    Directory of Open Access Journals (Sweden)

    Ian Salter

    Full Text Available Environmental DNA (eDNA can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA, a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs. Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can

  9. Long distance electron transport in marine sediments: Microbial and geochemical implications

    DEFF Research Database (Denmark)

    Risgaard-Petersen, Nils; Larsen, Steffen; Pfeffer, Christian

    redox half-reactions in distant regions of the sediment leads to formation of electrical fields, which modifies ion transport. The local proton producing and proton consuming half reactions induces pH extremes that accelerate dissolution of iron sulphides and calcium carbonates in anoxic layers...... and promotes the formation of Mg-calcite and iron oxides in the oxic zone. Oxygen seems to be the major electron acceptor, and more than 40% of the oxygen consumption in sediments can be driven by long distance electron transfer from distant electron donors. The major e-donor is sulfide, which is oxidized......-structural properties suggesting that they are living electric micro cables. The mode of action of these organisms has major impacts on element cycling by redox processes, pH balances, mineral dissolution/precipitations, and electro migration of ions in marine sediment. The ability of Desulfubulbus filaments to bridge...

  10. Using seabird habitat modeling to inform marine spatial planning in central California's National Marine Sanctuaries.

    Directory of Open Access Journals (Sweden)

    Jennifer McGowan

    Full Text Available Understanding seabird habitat preferences is critical to future wildlife conservation and threat mitigation in California. The objective of this study was to investigate drivers of seabird habitat selection within the Gulf of the Farallones and Cordell Bank National Marine Sanctuaries to identify areas for targeted conservation planning. We used seabird abundance data collected by the Applied California Current Ecosystem Studies Program (ACCESS from 2004-2011. We used zero-inflated negative binomial regression to model species abundance and distribution as a function of near surface ocean water properties, distances to geographic features and oceanographic climate indices to identify patterns in foraging habitat selection. We evaluated seasonal, inter-annual and species-specific variability of at-sea distributions for the five most abundant seabirds nesting on the Farallon Islands: western gull (Larus occidentalis, common murre (Uria aalge, Cassin's auklet (Ptychorampus aleuticus, rhinoceros auklet (Cerorhinca monocerata and Brandt's cormorant (Phalacrocorax penicillatus. The waters in the vicinity of Cordell Bank and the continental shelf east of the Farallon Islands emerged as persistent and highly selected foraging areas across all species. Further, we conducted a spatial prioritization exercise to optimize seabird conservation areas with and without considering impacts of current human activities. We explored three conservation scenarios where 10, 30 and 50 percent of highly selected, species-specific foraging areas would be conserved. We compared and contrasted results in relation to existing marine protected areas (MPAs and the future alternative energy footprint identified by the California Ocean Uses Atlas. Our results show that the majority of highly selected seabird habitat lies outside of state MPAs where threats from shipping, oil spills, and offshore energy development remain. This analysis accentuates the need for innovative marine

  11. Developing Model Benchtop Systems for Microbial Experimental Evolution

    Science.gov (United States)

    Gentry, D.; Wang, J.; Arismendi, D.; Alvarez, J.; Ouandji, C.; Blaich, J.

    2017-12-01

    Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA- damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO2 and O2. Additional

  12. Models of marine molluscan diseases: Trends and challenges.

    Science.gov (United States)

    Powell, Eric N; Hofmann, Eileen E

    2015-10-01

    Disease effects on host population dynamics and the transmission of pathogens between hosts are two important challenges for understanding how epizootics wax and wane and how disease influences host population dynamics. For the management of marine shellfish resources, marine diseases pose additional challenges in early intervention after the appearance of disease, management of the diseased population to limit a decline in host abundance, and application of measures to restrain that decline once it occurs. Mathematical models provide one approach for quantifying these effects and addressing the competing goals of managing the diseased population versus managing the disease. The majority of models for molluscan diseases fall into three categories distinguished by these competing goals. (1) Models that consider disease effects on the host population tend to focus on pathogen proliferation within the host. Many of the well-known molluscan diseases are pandemic, in that they routinely reach high prevalence rapidly over large geographic expanses, are characterized by transmission that does not depend upon a local source, and exert a significant influence on host population dynamics. Models focused on disease proliferation examine the influence of environmental change on host population metrics and provide a basis to better manage diseased stocks. Such models are readily adapted to questions of fishery management and habitat restoration. (2) Transmission models are designed to understand the mechanisms triggering epizootics, identify factors impeding epizootic development, and evaluate controls on the rate of disease spread over the host's range. Transmission models have been used extensively to study terrestrial diseases, yet little attention has been given to their potential for understanding the epidemiology of marine molluscan diseases. For management of diseases of wild stocks, transmission models open up a range of options, including the application of area

  13. Heterogeneity in Pure Microbial Systems: Experimental Measurements and Modeling.

    Science.gov (United States)

    González-Cabaleiro, Rebeca; Mitchell, Anca M; Smith, Wendy; Wipat, Anil; Ofiţeru, Irina D

    2017-01-01

    Cellular heterogeneity influences bioprocess performance in ways that until date are not completely elucidated. In order to account for this phenomenon in the design and operation of bioprocesses, reliable analytical and mathematical descriptions are required. We present an overview of the single cell analysis, and the mathematical modeling frameworks that have potential to be used in bioprocess control and optimization, in particular for microbial processes. In order to be suitable for bioprocess monitoring, experimental methods need to be high throughput and to require relatively short processing time. One such method used successfully under dynamic conditions is flow cytometry. Population balance and individual based models are suitable modeling options, the latter one having in particular a good potential to integrate the various data collected through experimentation. This will be highly beneficial for appropriate process design and scale up as a more rigorous approach may prevent a priori unwanted performance losses. It will also help progressing synthetic biology applications to industrial scale.

  14. Species Coexistence in Nitrifying Chemostats: A Model of Microbial Interactions

    Directory of Open Access Journals (Sweden)

    Maxime Dumont

    2016-12-01

    Full Text Available In a previous study, the two nitrifying functions (ammonia oxidizing bacteria (AOB or nitrite-oxidizing bacteria (NOB of a nitrification reactor—operated continuously over 525 days with varying inputs—were assigned using a mathematical modeling approach together with the monitoring of bacterial phylotypes. Based on these theoretical identifications, we develop here a chemostat model that does not explicitly include only the resources’ dynamics (different forms of soluble nitrogen but also explicitly takes into account microbial inter- and intra-species interactions for the four dominant phylotypes detected in the chemostat. A comparison of the models obtained with and without interactions has shown that such interactions permit the coexistence of two competing ammonium-oxidizing bacteria and two competing nitrite-oxidizing bacteria in competition for ammonium and nitrite, respectively. These interactions are analyzed and discussed.

  15. Microbial volatile communication in human organotypic lung models.

    Science.gov (United States)

    Barkal, Layla J; Procknow, Clare L; Álvarez-García, Yasmín R; Niu, Mengyao; Jiménez-Torres, José A; Brockman-Schneider, Rebecca A; Gern, James E; Denlinger, Loren C; Theberge, Ashleigh B; Keller, Nancy P; Berthier, Erwin; Beebe, David J

    2017-11-24

    We inhale respiratory pathogens continuously, and the subsequent signaling events between host and microbe are complex, ultimately resulting in clearance of the microbe, stable colonization of the host, or active disease. Traditional in vitro methods are ill-equipped to study these critical events in the context of the lung microenvironment. Here we introduce a microscale organotypic model of the human bronchiole for studying pulmonary infection. By leveraging microscale techniques, the model is designed to approximate the structure of the human bronchiole, containing airway, vascular, and extracellular matrix compartments. To complement direct infection of the organotypic bronchiole, we present a clickable extension that facilitates volatile compound communication between microbial populations and the host model. Using Aspergillus fumigatus, a respiratory pathogen, we characterize the inflammatory response of the organotypic bronchiole to infection. Finally, we demonstrate multikingdom, volatile-mediated communication between the organotypic bronchiole and cultures of Aspergillus fumigatus and Pseudomonas aeruginosa.

  16. Effects of short term feeding of some marine microalgae on the microbial profile associated with Dicentrarchus labrax post larvae

    Directory of Open Access Journals (Sweden)

    Heba S. El-Sayed

    2014-01-01

    Full Text Available This study investigates the microbial profile and antimicrobial activity of four marine microalgae species, Tetraselmis chuii, Nannochloropsis salina, Isochrysis galbana and Chlorella salina used in aquaculture of Dicentrarchus labrax in the post larval stage to estimate which was the best algal species that could be used as a green water technique and achieving the maximum rate of growth and survival of D. labrax post larvae. The results represented a significant increase in the length and width of D. labrax at p < 0.05 recorded in the case of enrichment with I. galbana followed by N. salina, and the most weight was recorded in the case of N. salina as compared with the control. Significant increase in percentage of survival of D. labrax was recorded in the case of C. salina and T. chuii (70% and 60.1%, respectively as compared with the control (22%. The antibacterial activity (AU of the different microalgal ethanolic extracts against fish indicator pathogens was determined. The results indicated that the ethanolic extracts of C. salina and T. chuii have the most positive records against the fish indicator pathogens (Escherichia coli, Pseudomonas aeruginosa, Vibrio damsela, Vibrio fluvialis and Aeromonas hydrophila. The current study was extended to determine the GC–MS of ethanolic extract of C. salina and T. chuii. The main constituents detected in the ethanolic extract were organic acids like hexadecanoic acid, octadecanoic acid, and an acyclic diterpene alcohol like phytol.

  17. Monitoring and modeling of microbial and biological water quality

    Science.gov (United States)

    Microbial and biological water quality informs on the health of water systems and their suitability for uses in irrigation, recreation, aquaculture, and other activities. Indicators of microbial and biological water quality demonstrate high spatial and temporal variability. Therefore, monitoring str...

  18. Methodology for modeling the microbial contamination of air filters.

    Directory of Open Access Journals (Sweden)

    Yun Haeng Joe

    Full Text Available In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter.

  19. Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

    Directory of Open Access Journals (Sweden)

    Reis Maria AM

    2008-07-01

    Full Text Available Abstract Background This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients. Results The model was validated with experimental data collected in a sequencing batch reactor (SBR operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments, and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i either with acetate or (ii with propionate as carbon source material. Metabolic flux analysis (MFA was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to ~0.17 C-mol/(C-mol.h. The results were compared with published pure culture metabolic studies. Conclusion Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of

  20. Results of the Marine Ice Sheet Model Intercomparison Project, MISMIP

    Directory of Open Access Journals (Sweden)

    F. Pattyn

    2012-05-01

    Full Text Available Predictions of marine ice-sheet behaviour require models that are able to robustly simulate grounding line migration. We present results of an intercomparison exercise for marine ice-sheet models. Verification is effected by comparison with approximate analytical solutions for flux across the grounding line using simplified geometrical configurations (no lateral variations, no effects of lateral buttressing. Unique steady state grounding line positions exist for ice sheets on a downward sloping bed, while hysteresis occurs across an overdeepened bed, and stable steady state grounding line positions only occur on the downward-sloping sections. Models based on the shallow ice approximation, which does not resolve extensional stresses, do not reproduce the approximate analytical results unless appropriate parameterizations for ice flux are imposed at the grounding line. For extensional-stress resolving "shelfy stream" models, differences between model results were mainly due to the choice of spatial discretization. Moving grid methods were found to be the most accurate at capturing grounding line evolution, since they track the grounding line explicitly. Adaptive mesh refinement can further improve accuracy, including fixed grid models that generally perform poorly at coarse resolution. Fixed grid models, with nested grid representations of the grounding line, are able to generate accurate steady state positions, but can be inaccurate over transients. Only one full-Stokes model was included in the intercomparison, and consequently the accuracy of shelfy stream models as approximations of full-Stokes models remains to be determined in detail, especially during transients.

  1. The Vineyard Yeast Microbiome, a Mixed Model Microbial Map

    Science.gov (United States)

    Setati, Mathabatha Evodia; Jacobson, Daniel; Andong, Ursula-Claire; Bauer, Florian

    2012-01-01

    Vineyards harbour a wide variety of microorganisms that play a pivotal role in pre- and post-harvest grape quality and will contribute significantly to the final aromatic properties of wine. The aim of the current study was to investigate the spatial distribution of microbial communities within and between individual vineyard management units. For the first time in such a study, we applied the Theory of Sampling (TOS) to sample gapes from adjacent and well established commercial vineyards within the same terroir unit and from several sampling points within each individual vineyard. Cultivation-based and molecular data sets were generated to capture the spatial heterogeneity in microbial populations within and between vineyards and analysed with novel mixed-model networks, which combine sample correlations and microbial community distribution probabilities. The data demonstrate that farming systems have a significant impact on fungal diversity but more importantly that there is significant species heterogeneity between samples in the same vineyard. Cultivation-based methods confirmed that while the same oxidative yeast species dominated in all vineyards, the least treated vineyard displayed significantly higher species richness, including many yeasts with biocontrol potential. The cultivatable yeast population was not fully representative of the more complex populations seen with molecular methods, and only the molecular data allowed discrimination amongst farming practices with multivariate and network analysis methods. Importantly, yeast species distribution is subject to significant intra-vineyard spatial fluctuations and the frequently reported heterogeneity of tank samples of grapes harvested from single vineyards at the same stage of ripeness might therefore, at least in part, be due to the differing microbiota in different sections of the vineyard. PMID:23300721

  2. 3D Marine MT Modeling for a Topographic Seafloor

    Science.gov (United States)

    Zhang, B., Sr.; Yin, C.; Ren, X.; Liu, Y.; Huang, X.; Liu, L.

    2017-12-01

    As an effective geophysical tool, marine magnetotelluric (MMT) exploration has been widely used in offshore oil and gas exploration. Accordingly, the MMT forward modelling has made big progress. However, most of the researches are focused on a flat seafloor. In this paper, we present a 3D finite-element (FE) algorithm for marine MT forward modelling based on unstructured grids that can accurately model the MMT responses for a topographic seafloor. The boundary value problem for the forward modelling is described by an Helmholtz equation together with the boundary conditions derived by assuming the electrical polarizations respectively along the x- and y-direction on the top surface of the modelling domain. Applying the Galerkin method to the boundary value problem and substituting the unstructured finite-element vector shape function into the equation, we derive the final large linear system for the two polarizations, from which the EM fields is obtained for the calculation of impedance apparent resistivities and phases. To verify the effectiveness of our algorithm, we compare our modelling results with those by Key's (2013) 2D marine MT open source code of Scripps Institution of Oceanography (Figure 1). From Figure 1, one sees that the two agree well, implying that our 3D modelling method based unstructured FE is an effective modelling tool for topographic seafloor. From the MMT modelling responses for other topographic seafloor models (not shown here), we further observe that 1) the apparent resistivities have a similar profile pattern to the topography at the seafloor; 2) at the edges of the topography, there exist sharp changes; 3) the seafloor topography may dominate the responses from the abnormal bodies under the seafloor. This paper is supported by Key Program of National Natural Science Foundation of China (41530320), China Natural Science Foundation for Young Scientists (41404093), and Key National Research Project of China (2016YFC0303100, 2017YFC0601900)

  3. Damped trophic cascades driven by fishing in model marine ecosystems

    DEFF Research Database (Denmark)

    Andersen, Ken Haste; Pedersen, Martin

    2010-01-01

    The largest perturbation on upper trophic levels of many marine ecosystems stems from fishing. The reaction of the ecosystem goes beyond the trophic levels directly targeted by the fishery. This reaction has been described either as a change in slope of the overall size spectrum or as a trophic...... cascade triggered by the removal of top predators. Here we use a novel size- and trait-based model to explore how marine ecosystems might react to perturbations from different types of fishing pressure. The model explicitly resolves the whole life history of fish, from larvae to adults. The results show...... that fishing does not change the overall slope of the size spectrum, but depletes the largest individuals and induces trophic cascades. A trophic cascade can propagate both up and down in trophic levels driven by a combination of changes in predation mortality and food limitation. The cascade is damped...

  4. Managing the Marine Environment, Conceptual Models and Assessment Considerations for the European Marine Strategy Framework Directive

    Directory of Open Access Journals (Sweden)

    Christopher John Smith

    2016-08-01

    Full Text Available Conceptual models summarize, visualize and explain actual or predicted situations and how they might be tackled. In recent years, Pressure-State-Response (P-S-R frameworks have been central to conceptualizing marine ecosystem issues and then translating those to stakeholders, environmental managers and researchers. Society is concerned about the risks to the natural and human system posed by those Pressures (thus needing risk assessment and then needs to act to minimize or compensate those risks (as risk management. This research relates this to the DPSIR (Drivers-Pressure-State(change-Impact-Response hierarchical framework using standardized terminology/definitions and lists of impacting Activities and Pressures affecting ecosystem components, incorporating the European Marine Strategy Framework Directive (MSFD legal decision components. This uses the example of fishing activity and the pressure of trawling from abrasion on the seabed and its effects on particular components. The mechanisms of Pressure acting on State changes are highlighted here as an additional refinement to DPSIR. The approach moves from conceptual models to actual assessments including: assessment methodologies (interactive matrices, ecosystem modeling, Bayesian Belief Networks, Bow-tie approach, some assessment tools data availability, confidence, scaling, cumulative effects and multiple simultaneous Pressures, which more often occur in multi-use and multi-user areas. In defining and describing the DPSIR Conceptual Framework we consider its use in re-world ecosystems affected by multiple pressures or multiple mechanisms of single pressures, and show how it facilitates management and assessment issues with particular relevance to the MSFD.

  5. Microbial surfactant mediated degradation of anthracene in aqueous phase by marine Bacillus licheniformis MTCC 5514

    Directory of Open Access Journals (Sweden)

    Sreethar Swaathy

    2014-12-01

    Full Text Available The present study emphasizes the biosurfactant mediated anthracene degradation by a marine alkaliphile Bacillus licheniformis (MTCC 5514. The isolate, MTCC 5514 degraded >95% of 300 ppm anthracene in an aqueous medium within 22 days and the degradation percentage reduced significantly when the concentration of anthracene increased to above 500 ppm. Naphthalene, naphthalene 2-methyl, phthalic acid and benzene acetic acid are the products of degradation identified based on thin layer chromatography, high performance liquid chromatography, gas chromatography and mass analyses. It has been observed that the degradation is initiated by the biosurfactant of the isolate for solubilization through micellation and then the alkali pH and intra/extra cellular degradative enzymes accomplish the degradation process. Encoding of genes responsible for biosurfactant production (licA3 as well as catabolic reactions (C23O made with suitable primers designed. The study concludes in situ production of biosurfactant mediates the degradation of anthracene by B. licheniformis.

  6. Tourism Operator Sustainability Predictive Model in Marine Park

    OpenAIRE

    Mohamad, Zaleha; Ramli, Nurhafizah; Muslim, Aidy Mohamed Shawal M.; Hii, Yii Siang

    2017-01-01

    Sustainable tourism is the concept of visiting a place as a tourist and trying to make only a positive impact on the environment, society and economy. Tourism can involve primary transportation to the general location, local transportation, accommodations, entertainment, recreation, nourishment and shopping. In this context, the research study tourism is operator towards recreational. This study analyzed the sustainability tourism predictive model towards operator in marine park. The research...

  7. Modeling of Nonlinear Marine Cooling Systems with Closed Circuit Flow

    DEFF Research Database (Denmark)

    Hansen, Michael; Stoustrup, Jakob; Bendtsen, Jan Dimon

    2011-01-01

    We consider the problem of constructing a mathematical model for a specific type of marine cooling system. The system in question is used for cooling the main engine and main engine auxiliary components, such as diesel generators, turbo chargers and main engine air coolers for certain classes...... of container ships. The purpose of the model is to describe the important dynamics of the system, such as nonlinearities, transport delays and closed circuit flow dynamics to enable the model to be used for control design and simulation. The control challenge is related to the highly non-standard type of step...

  8. Order reduction for a model of marine bacteriophage evolution

    Science.gov (United States)

    Pagliarini, Silvia; Korobeinikov, Andrei

    2017-02-01

    A typical mechanistic model of viral evolution necessary includes several time scales which can differ by orders of magnitude. Such a diversity of time scales makes analysis of these models difficult. Reducing the order of a model is highly desirable when handling such a model. A typical approach applied to such slow-fast (or singularly perturbed) systems is the time scales separation technique. Constructing the so-called quasi-steady-state approximation is the usual first step in applying the technique. While this technique is commonly applied, in some cases its straightforward application can lead to unsatisfactory results. In this paper we construct the quasi-steady-state approximation for a model of evolution of marine bacteriophages based on the Beretta-Kuang model. We show that for this particular model the quasi-steady-state approximation is able to produce only qualitative but not quantitative fit.

  9. Modeling marine surface microplastic transport to assess optimal removal locations

    International Nuclear Information System (INIS)

    Sherman, Peter; Van Sebille, Erik

    2016-01-01

    Marine plastic pollution is an ever-increasing problem that demands immediate mitigation and reduction plans. Here, a model based on satellite-tracked buoy observations and scaled to a large data set of observations on microplastic from surface trawls was used to simulate the transport of plastics floating on the ocean surface from 2015 to 2025, with the goal to assess the optimal marine microplastic removal locations for two scenarios: removing the most surface microplastic and reducing the impact on ecosystems, using plankton growth as a proxy. The simulations show that the optimal removal locations are primarily located off the coast of China and in the Indonesian Archipelago for both scenarios. Our estimates show that 31% of the modeled microplastic mass can be removed by 2025 using 29 plastic collectors operating at a 45% capture efficiency from these locations, compared to only 17% when the 29 plastic collectors are moored in the North Pacific garbage patch, between Hawaii and California. The overlap of ocean surface microplastics and phytoplankton growth can be reduced by 46% at our proposed locations, while sinks in the North Pacific can only reduce the overlap by 14%. These results are an indication that oceanic plastic removal might be more effective in removing a greater microplastic mass and in reducing potential harm to marine life when closer to shore than inside the plastic accumulation zones in the centers of the gyres. (letter)

  10. Spatio-temporal patterns in simple models of marine systems

    Science.gov (United States)

    Feudel, U.; Baurmann, M.; Gross, T.

    2009-04-01

    Spatio-temporal patterns in marine systems are a result of the interaction of population dynamics with physical transport processes. These physical transport processes can be either diffusion processes in marine sediments or in the water column. We study the dynamics of one population of bacteria and its nutrient in in a simplified model of a marine sediments, taking into account that the considered bacteria possess an active as well as an inactive state, where activation is processed by signal molecules. Furthermore the nutrients are transported actively by bioirrigation and passively by diffusion. It is shown that under certain conditions Turing patterns can occur which yield heterogeneous spatial patterns of the species. The influence of bioirrigation on Turing patterns leads to the emergence of ''hot spots``, i.e. localized regions of enhanced bacterial activity. All obtained patterns fit quite well to observed patterns in laboratory experiments. Spatio-temporal patterns appear in a predator-prey model, used to describe plankton dynamics. These patterns appear due to the simultaneous emergence of Turing patterns and oscillations in the species abundance in the neighborhood of a Turing-Hopf bifurcation. We observe a large variety of different patterns where i) stationary heterogeneous patterns (e.g. hot and cold spots) compete with spatio-temporal patterns ii) slowly moving patterns are embedded in an oscillatory background iii) moving fronts and spiral waves appear.

  11. Modeling marine surface microplastic transport to assess optimal removal locations

    Science.gov (United States)

    Sherman, Peter; van Sebille, Erik

    2016-01-01

    Marine plastic pollution is an ever-increasing problem that demands immediate mitigation and reduction plans. Here, a model based on satellite-tracked buoy observations and scaled to a large data set of observations on microplastic from surface trawls was used to simulate the transport of plastics floating on the ocean surface from 2015 to 2025, with the goal to assess the optimal marine microplastic removal locations for two scenarios: removing the most surface microplastic and reducing the impact on ecosystems, using plankton growth as a proxy. The simulations show that the optimal removal locations are primarily located off the coast of China and in the Indonesian Archipelago for both scenarios. Our estimates show that 31% of the modeled microplastic mass can be removed by 2025 using 29 plastic collectors operating at a 45% capture efficiency from these locations, compared to only 17% when the 29 plastic collectors are moored in the North Pacific garbage patch, between Hawaii and California. The overlap of ocean surface microplastics and phytoplankton growth can be reduced by 46% at our proposed locations, while sinks in the North Pacific can only reduce the overlap by 14%. These results are an indication that oceanic plastic removal might be more effective in removing a greater microplastic mass and in reducing potential harm to marine life when closer to shore than inside the plastic accumulation zones in the centers of the gyres.

  12. Modeling Marine Electromagnetic Survey with Radial Basis Function Networks

    Directory of Open Access Journals (Sweden)

    Agus Arif

    2011-08-01

    Full Text Available A marine electromagnetic survey is an engineering endeavour to discover the location and dimension of a hydrocarbon layer under an ocean floor. In this kind of survey, an array of electric and magnetic receivers are located on the sea floor and record the scattered, refracted and reflected electromagnetic wave, which has been transmitted by an electric dipole antenna towed by a vessel. The data recorded in receivers must be processed and further analysed to estimate the hydrocarbon location and dimension. To conduct those analyses successfuly, a radial basis function (RBF network could be employed to become a forward model of the input-output relationship of the data from a marine electromagnetic survey. This type of neural networks is working based on distances between its inputs and predetermined centres of some basis functions. A previous research had been conducted to model the same marine electromagnetic survey using another type of neural networks, which is a multi layer perceptron (MLP network. By comparing their validation and training performances (mean-squared errors and correlation coefficients, it is concluded that, in this case, the MLP network is comparatively better than the RBF network

  13. Spatiotemporal modelling of marine movement data using Template Model Builder (TMB)

    DEFF Research Database (Denmark)

    Auger-Méthé, Marie; Albertsen, Christoffer Moesgaard; Jonsen, Ian D.

    2017-01-01

    Tracking of marine animals has increased exponentially in the past decade, and the resulting data could lead to an in-depth understanding of the causes and consequences of movement in the ocean. However, most common marine tracking systems are associated with large measurement errors. Accounting...... for these errors requires the use of hierarchical models, which are often difficult to fit to data. Using 3 case studies, we demonstrate that Template Model Builder (TMB), a new R package, is an accurate, efficient and flexible framework for modelling movement data. First, to demonstrate that TMB is as accurate...... tool for modelling marine movement data. We discuss how TMB’s potential reaches beyond marine movement studies...

  14. Requirements for modeling airborne microbial contamination in space stations

    Science.gov (United States)

    Van Houdt, Rob; Kokkonen, Eero; Lehtimäki, Matti; Pasanen, Pertti; Leys, Natalie; Kulmala, Ilpo

    2018-03-01

    Exposure to bioaerosols is one of the facets that affect indoor air quality, especially for people living in densely populated or confined habitats, and is associated to a wide range of health effects. Good indoor air quality is thus vital and a prerequisite for fully confined environments such as space habitats. Bioaerosols and microbial contamination in these confined space stations can have significant health impacts, considering the unique prevailing conditions and constraints of such habitats. Therefore, biocontamination in space stations is strictly monitored and controlled to ensure crew and mission safety. However, efficient bioaerosol control measures rely on solid understanding and knowledge on how these bioaerosols are created and dispersed, and which factors affect the survivability of the associated microorganisms. Here we review the current knowledge gained from relevant studies in this wide and multidisciplinary area of bioaerosol dispersion modeling and biological indoor air quality control, specifically taking into account the specific space conditions.

  15. Investigating microbial cycling of recalcitrant organic matter in marine sediments using natural isotope respirometry in a novel, carbon-free bioreactor

    Science.gov (United States)

    Mahmoudi, N.; Beaupre, S. R.; Pearson, A.

    2016-02-01

    Marine sediments harbor complex microbial communities that play a key role in the cycling of carbon and nutrients. Reactions initiated by microbial enzymes at the molecular scale drive the rate and extent of organic matter degradation to CO2 and CH4. Organic matter is comprised of multiple carbon pools with different intrinsic turnover times. It is hypothesized that microbes will degrade younger pools with more labile compounds, while older pools with refractory compounds will remain unutilized. However, many studies have shown that microbes are capable of respiring older, refractory pools of organic matter in a number of environments. In order to better understand microbial carbon cycling and the fate of recalcitrant organic matter, we constructed a novel bioreactor system to measure carbon isotopes during microbial degradation of complex organic matter. This system enables us to measure the natural isotopic signature (δ13C and Δ14C ) of microbially-respired CO2, thereby allowing us to determine the age of the organic matter that is being respired. We investigated microbial carbon utilization in sediments from Falmouth, MA and observed a pattern of successive microbial respiration such that several peaks appear over the course of a 7-day incubation. Δ14C signatures of CO2 fractions collected during incubation ranged from -185 to +70‰ with the majority of CO2 appearing to be modern. This indicates that the microbial community is primarily are respiring labile organic matter from fast cycling pools. Interestingly, the observation of multiple peaks with similar Δ14C signatures suggests that organic matter is degraded in a step-wise manner by a succession of microbial taxa. Illumina sequencing of 16S rRNA genes will identify these successions of bacteria (and archaea), while enzymatic analyses may help determine the metabolic pathways that correspond to each peak. Our study will provide a molecular-level framework for organic matter degradation and provide

  16. Modelling the marine advance of the last Cordilleran ice sheet

    Science.gov (United States)

    Seguinot, Julien; Rogozhina, Irina

    2014-05-01

    Marine advance of the last Cordilleran ice sheet onto the north-eastern Pacific continental shelf may have caused rapid fluctuations of sea level and potentially impacted upon human migration into North America. However the position of the former ice front was critically controlled by a process that remains poorly understood: glacier calving. Geomorphological reconstructions show that part of the presently oceanic areas were ice-covered, allowing for downstream formation of the well-studied Puget and Juan de Fuca lobes. Here we use a numerical glacier model (PISM) to reconstruct the former marine front of the Cordilleran ice sheet and its impact on upstream ice dynamics. Our simulations show that the use of a thickness-based calving law leads to a strong deficit of marine ice cover in the areas where existing reconstructions suggest its advance. In contrast, a physically-based parametrization of glacier calving using the main components of the strain rate tensor (eigencalving; A. Levermann, T. Albrecht, R. Winkelmann, M. A. Martin, M. Haseloff, and I. Joughin, The Cryosphere, 6, 273-286, 2012) reproduces the geomorphologically inferred ice extent.

  17. Modelling light and photosynthesis in the marine environment

    Directory of Open Access Journals (Sweden)

    Bogdan Woźniak

    2003-06-01

    Full Text Available The overriding and far-reaching aim of our work has been to achieve a good understanding of the processes of light interaction with phytoplankton in the sea and to develop an innovative physical model of photosynthesis in the marine environment, suitable for the remote sensin gof marine primary production. Unlike previous models, the present one takesgreater account of the complexity of the physiological processes in phytoplankton. We have focused in particular on photophysiological processes, which are governed directly or indirectly by light energy, or in which light, besides the nutrient content in and the temperature of seawater, is one of the principal limiting factors.    To achieve this aim we have carried out comprehensive statistical analyses of the natural variability of the main photophysiological properties of phytoplankton and their links with the principal abiotic factors in the sea. These analyses have made use of extensive empirical data gathered in a wide diversity of seas and oceans by Polish and Russian teams as well as by joint Polish-Russian expeditions. Data sets available on the Internet have also been applied. As a result, a set of more or less complex, semi-empirical models of light-stimulated processes occurring in marine phytoplankton cells has been developed. The trophic type of sea, photo-acclimation and the production of photoprotecting carotenoids, chromatic acclimation and the production of various forms of chlorophyll-antennas and photosynthetic carotenoids, cell adaptation by the package effect, light absorption, photosynthesis, photoinhibition, the fluorescence effect, and the activation of PS2 centres are all considered in the models. These take into account not only the influence of light, but also, indirectly, that of the vertical mixing of water; in the case of photosynthesis, the quantum yield has been also formulated as being dependent on the nutrient concentrations and the temperature of seawater

  18. Acoustic Propagation Modeling for Marine Hydro-Kinetic Applications

    Science.gov (United States)

    Johnson, C. N.; Johnson, E.

    2014-12-01

    The combination of riverine, tidal, and wave energy have the potential to supply over one third of the United States' annual electricity demand. However, in order to deploy and test prototypes, and commercial installations, marine hydrokinetic (MHK) devices must meet strict regulatory guidelines that determine the maximum amount of noise that can be generated and sets particular thresholds for determining disturbance and injury caused by noise. An accurate model for predicting the propagation of a MHK source in a real-life hydro-acoustic environment has been established. This model will help promote the growth and viability of marine, water, and hydrokinetic energy by confidently assuring federal regulations are meet and harmful impacts to marine fish and wildlife are minimal. Paracousti, a finite difference solution to the acoustic equations, was originally developed for sound propagation in atmospheric environments and has been successfully validated for a number of different geophysical activities. The three-dimensional numerical implementation is advantageous over other acoustic propagation techniques for a MHK application where the domains of interest have complex 3D interactions from the seabed, banks, and other shallow water effects. A number of different cases for hydro-acoustic environments have been validated by both analytical and numerical results from canonical and benchmark problems. This includes a variety of hydrodynamic and physical environments that may be present in a potential MHK application including shallow and deep water, sloping, and canyon type bottoms, with varying sound speed and density profiles. With the model successfully validated for hydro-acoustic environments more complex and realistic MHK sources from turbines and/or arrays can be modeled.

  19. Microcosm Experiments and Modeling of Microbial Movement Under Unsaturated Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Brockman, F.J.; Kapadia, N.; Williams, G.; Rockhold, M.

    2006-04-05

    Colonization of bacteria in porous media has been studied primarily in saturated systems. In this study we examine how microbial colonization in unsaturated porous media is controlled by water content and particle size. This is important for understanding the feasibility and success of bioremediation via nutrient delivery when contaminant degraders are at low densities and when total microbial populations are sparse and spatially discontinuous. The study design used 4 different sand sizes, each at 4 different water contents; experiments were run with and without acetate as the sole carbon source. All experiments were run in duplicate columns and used the motile organism Pseudomonas stutzeri strain KC, a carbon tetrachloride degrader. At a given sand size, bacteria traveled further with increasing volumetric water content. At a given volumetric water content, bacteria generally traveled further with increasing sand size. Water redistribution, solute transport, gas diffusion, and bacterial colonization dynamics were simulated using a numerical finite-difference model. Solute and bacterial transport were modeled using advection-dispersion equations, with reaction rate source/sink terms to account for bacterial growth and substrate utilization, represented using dual Monod-type kinetics. Oxygen transport and diffusion was modeled accounting for equilibrium partitioning between the aqueous and gas phases. The movement of bacteria in the aqueous phase was modeled using a linear impedance model in which the term D{sub m} is a coefficient, as used by Barton and Ford (1995), representing random motility. The unsaturated random motility coefficients we obtained (1.4 x 10{sup -6} to 2.8 x 10{sup -5} cm{sup 2}/sec) are in the same range as those found by others for saturated systems (3.5 x 10{sup -6} to 3.5 x 10{sup -5} cm{sup 2}/sec). The results show that some bacteria can rapidly migrate in well sorted unsaturated sands (and perhaps in relatively high porosity, poorly

  20. Complete modeling for systems of a marine diesel engine

    Science.gov (United States)

    Nahim, Hassan Moussa; Younes, Rafic; Nohra, Chadi; Ouladsine, Mustapha

    2015-03-01

    This paper presents a simulator model of a marine diesel engine based on physical, semi-physical, mathematical and thermodynamic equations, which allows fast predictive simulations. The whole engine system is divided into several functional blocks: cooling, lubrication, air, injection, combustion and emissions. The sub-models and dynamic characteristics of individual blocks are established according to engine working principles equations and experimental data collected from a marine diesel engine test bench for SIMB Company under the reference 6M26SRP1. The overall engine system dynamics is expressed as a set of simultaneous algebraic and differential equations using sub-blocks and S-Functions of Matlab/Simulink. The simulation of this model, implemented on Matlab/Simulink has been validated and can be used to obtain engine performance, pressure, temperature, efficiency, heat release, crank angle, fuel rate, emissions at different sub-blocks. The simulator will be used, in future work, to study the engine performance in faulty conditions, and can be used to assist marine engineers in fault diagnosis and estimation (FDI) as well as designers to predict the behavior of the cooling system, lubrication system, injection system, combustion, emissions, in order to optimize the dimensions of different components. This program is a platform for fault simulator, to investigate the impact on sub-blocks engine's output of changing values for faults parameters such as: faulty fuel injector, leaky cylinder, worn fuel pump, broken piston rings, a dirty turbocharger, dirty air filter, dirty air cooler, air leakage, water leakage, oil leakage and contamination, fouling of heat exchanger, pumps wear, failure of injectors (and many others).

  1. Predictions and Verification of an Isotope Marine Boundary Layer Model

    Science.gov (United States)

    Feng, X.; Posmentier, E. S.; Sonder, L. J.; Fan, N.

    2017-12-01

    A one-dimensional (1D), steady state isotope marine boundary layer (IMBL) model is constructed. The model includes meteorologically important features absent in Craig and Gordon type models, namely height-dependent diffusion/mixing and convergence of subsiding external air. Kinetic isotopic fractionation results from this height-dependent diffusion which starts as pure molecular diffusion at the air-water interface and increases linearly with height due to turbulent mixing. The convergence permits dry, isotopically depleted air subsiding adjacent to the model column to mix into ambient air. In δD-δ18O space, the model results fill a quadrilateral, of which three sides represent 1) vapor in equilibrium with various sea surface temperatures (SSTs) (high d18O boundary of quadrilateral); 2) mixture of vapor in equilibrium with seawater and vapor in the subsiding air (lower boundary depleted in both D and 18O); and 3) vapor that has experienced the maximum possible kinetic fractionation (high δD upper boundary). The results can be plotted in d-excess vs. δ18O space, indicating that these processes all cause variations in d-excess of MBL vapor. In particular, due to relatively high d-excess in the descending air, mixing of this air into the MBL causes an increase in d-excess, even without kinetic isotope fractionation. The model is tested by comparison with seven datasets of marine vapor isotopic ratios, with excellent correspondence; >95% of observational data fall within the quadrilateral area predicted by the model. The distribution of observations also highlights the significant influence of vapor from the nearby converging descending air on isotopic variations in the MBL. At least three factors may explain the affect the isotopic composition of precipitation. The model can be applied to modern as well as paleo- climate conditions.

  2. Boundary layer models for calving marine outlet glaciers

    Directory of Open Access Journals (Sweden)

    C. Schoof

    2017-10-01

    Full Text Available We consider the flow of marine-terminating outlet glaciers that are laterally confined in a channel of prescribed width. In that case, the drag exerted by the channel side walls on a floating ice shelf can reduce extensional stress at the grounding line. If ice flux through the grounding line increases with both ice thickness and extensional stress, then a longer shelf can reduce ice flux by decreasing extensional stress. Consequently, calving has an effect on flux through the grounding line by regulating the length of the shelf. In the absence of a shelf, it plays a similar role by controlling the above-flotation height of the calving cliff. Using two calving laws, one due to Nick et al. (2010 based on a model for crevasse propagation due to hydrofracture and the other simply asserting that calving occurs where the glacier ice becomes afloat, we pose and analyse a flowline model for a marine-terminating glacier by two methods: direct numerical solution and matched asymptotic expansions. The latter leads to a boundary layer formulation that predicts flux through the grounding line as a function of depth to bedrock, channel width, basal drag coefficient, and a calving parameter. By contrast with unbuttressed marine ice sheets, we find that flux can decrease with increasing depth to bedrock at the grounding line, reversing the usual stability criterion for steady grounding line location. Stable steady states can then have grounding lines located on retrograde slopes. We show how this anomalous behaviour relates to the strength of lateral versus basal drag on the grounded portion of the glacier and to the specifics of the calving law used.

  3. Modeling of Unsteady Sheet Cavitation on Marine Propeller Blades

    Directory of Open Access Journals (Sweden)

    Spyros A. Kinnas

    2003-01-01

    Full Text Available Unsteady sheet cavitation is very common on marine propulsor blades. The authors summarize a lifting-surface and a surface-panel model to solve for the unsteady cavitating flow around a propeller that is subject to nonaxisymmetric inflow. The time-dependent extent and thickness of the cavity were determined by using an iterative method. The cavity detachment was determined by applying the smooth detachment criterion in an iterative manner. A nonzeroradius developed vortex cavity model was utilized at the tip of the blade, and the trailing wake geometry was determined using a fully unsteady wake-alignment process. Comparisons of predictions by the two models and measurements from several experiments are given.

  4. Quantification of Model Uncertainty in Modeling Mechanisms of Soil Microbial Respiration Pulses to Simulate Birch Effect

    Science.gov (United States)

    Elshall, A. S.; Ye, M.; Niu, G. Y.; Barron-Gafford, G.

    2014-12-01

    A Bayesian framework is developed to quantify predictive uncertainty in environmental modeling caused by uncertainty in modeling scenarios, model structures, model parameters, and data. An example of using the framework to quantify model uncertainty is presented to simulate soil microbial respiration pulses in response to episodic rainfall pulses (the "Birch effect"). A total of five models are developed; they evolve from an existing four-carbon (C) pool model to models with additional C pools and recently developed models with explicit representations of soil moisture controls on C degradation and microbial uptake rates. Markov chain Monte Carlo (MCMC) methods with generalized likelihood function (not Gaussian) are used to estimate posterior parameter distributions of the models, and the posterior parameter samples are used to evaluate probabilities of the models. The models with explicit representations of soil moisture controls outperform the other models. The models with additional C pools for accumulation of degraded C in the dry zone of the soil pore space result in a higher probability of reproducing the observed Birch pulses. A cross-validation is conducted to explore predictive performance of model averaging and of individual models. The Bayesian framework is mathematically general and can be applied to a wide range of environmental problems.

  5. Capturing microbial sources distributed in a mixed-use watershed within an integrated environmental modeling workflow

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few provide loading rates on land surfaces and point sources to the waterbody network. This paper describes the underlying equations for microbial loading rates associated with 1) land-applied ...

  6. Density-dependent microbial turnover improves soil carbon model predictions of long-term litter manipulations

    Science.gov (United States)

    Georgiou, Katerina; Abramoff, Rose; Harte, John; Riley, William; Torn, Margaret

    2017-04-01

    Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity via abiotic effects on soil or mediated by changes in plant inputs. Recently, many promising microbial models of soil organic carbon (SOC) decomposition have been proposed to advance understanding and prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the sources of instability in four models that span the range of complexity of these recent microbial models, by sequentially adding complexity to a simple model to include microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We propose a formulation that introduces density-dependence of microbial turnover, which acts to limit population sizes and reduce oscillations. We compare these models to results from 24 long-term C-input field manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that widely used first-order models and microbial models without density-dependence cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures. The proposed formulation improves predictions of long-term C-input changes, and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to common microbial models. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in Earth System Models.

  7. Modelling microbial metabolic rewiring during growth in a complex medium.

    Science.gov (United States)

    Fondi, Marco; Bosi, Emanuele; Presta, Luana; Natoli, Diletta; Fani, Renato

    2016-11-24

    In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now. We used multi-step constraint-based metabolic modelling to simulate the growth in a complex medium over several time steps of the Antarctic model organism Pseudoalteromonas haloplanktis TAC125. As each of these phases is characterized by a specific set of amino acids to be used as carbon and energy source our modelling framework describes the major consequences of nutrients switching at the system level. The model predicts that a deep metabolic reprogramming might be required to achieve optimal biomass production in different stages of growth (different medium composition), with at least half of the cellular metabolic network involved (more than 50% of the metabolic genes). Additionally, we show that our modelling framework is able to capture metabolic functional association and/or common regulatory features of the genes embedded in our reconstruction (e.g. the presence of common regulatory motifs). Finally, to explore the possibility of a sub-optimal biomass objective function (i.e. that cells use resources in alternative metabolic processes at the expense of optimal growth) we have implemented a MOMA-based approach (called nutritional-MOMA) and compared the outcomes with those obtained with Flux Balance Analysis (FBA). Growth simulations under this scenario revealed the deep impact of

  8. Probabilistic Estimates of Global Marine N2O Emissions within the Bern3D Earth System Model of Intermediate Complexity

    Science.gov (United States)

    Keller, K. M.; Battaglia, G.; Joos, F.

    2016-02-01

    Nitrous oxide (N2O) is a radiatively active atmospheric trace gas (currently 325 ppb, increasing by 0.25% yr-1) and is emitted to the atmosphere from poorly constrained microbial processes on land and in the oceans. The latest estimates given by the IPCC for marine N2O sources range from 1.8-9.4 TgN yr-1. Marine N2O production is commonly parameterized as a function of organic matter remineralization, oxygen concentrations, or temperature to account for (chemo-autotrophic) nitrification and (chemo-heterotrophic) denitrification processes. We implemented different production schemes in the cost-efficient Bern3D Earth-System Model of Intermediate Complexity which features a 3-D frictional-geostrophic ocean and an OCMIP2-type marine carbon cycle. We optimize the parameters governing N2O production in a probabilistic, Monte-Carlo-type, Bayesian framework by applying observed dissolved N2O data, compiled in the MEMENTO database, as constraints. N2O emissions of the observation-constrained model ensemble will then be determined for both future and past (e.g. Younger-Dryas) environmental conditions.

  9. Riverine Dissolved Organic Matter Degradation Modeled Through Microbial Incubations of Vascular Plant Leachates

    Science.gov (United States)

    Harfmann, J.; Hernes, P.; Chuang, C. Y.

    2015-12-01

    Dissolved organic matter (DOM) contains as much carbon as is in the atmosphere, provides the main link between terrestrial and marine carbon reservoirs, and fuels the microbial food web. The fate and removal of DOM is a result of several complex conditions and processes, including photodegradation, sorption/desorption, dominant vascular plant sources, and microbial abundance. In order to better constrain factors affecting microbial degradation, laboratory incubations were performed using Sacramento River water for microbial inoculums and vascular plant leachates. Four vascular plant sources were chosen based on their dominance in the Sacramento River Valley: gymnosperm needles from Pinus sabiniana (foothill pine), angiosperm dicot leaves from Quercus douglassi (blue oak), angiosperm monocot mixed annual grasses, and angiosperm monocot mixed Schoenoplectus acutus (tule) and Typha spp. (cattails). Three concentrations of microbial inoculum were used for each plant material, ranging from 0.2% to 10%. Degradation was monitored as a function of time using dissolved organic carbon (DOC), UV-Vis absorbance, and fluorescent dissolved organic matter (fDOM), and was compared across vascular plant type and inoculum concentration.

  10. Modelling the dispersion and scavenging of plutonium in marine systems

    International Nuclear Information System (INIS)

    Nakano, Masanao

    2003-01-01

    An Oceanic General Circulation Model (OGCM) has been developed for modelling the dispersion of plutonium (Pu) and other non-conservative tracers in the marine system. A plutonium scavenging model as well as an advection-diffusion model has been incorporated into the OGCM. It appears that the best way to validate a numerical model for the dispersion of non-conservative tracers in the global ocean would be to calculate radionuclide concentrations in the ocean from atmospheric nuclear tests (global and local fallout) and to compare them with observations. This paper concentrates on predictions of the distributions and vertical profiles of 239,240 Pu in the water column of the Pacific Ocean, both from global fallout as well as from local fallout from nuclear weapons tests at Bikini and Enewetak Atolls. The water profile concentrations, water and sediment inventories of 239,240 Pu have shown generally good agreement between calculated and observed data. Nevertheless, the present model cannot calculate the water profiles in the north North Pacific or the west coast of the American continent very well, mainly because of the underestimation of the effect of biological productivity on Pu scavenging and its removal from the water column in these regions. (author)

  11. Changes in microbial composition and the prevalence of foodborne pathogens in crab marinated in soy sauce produced by six manufacturing plants.

    Science.gov (United States)

    Kim, Sun Ae; Choi, Eun Sook; Kim, Nam Hee; Kim, Hye Won; Lee, Na Young; Cho, Tae Jin; Jo, Jun Il; Kim, Soon Han; Lee, Soon Ho; Ha, Sang Do; Rhee, Min Suk

    2017-04-01

    The present study examined the changes in microbiological composition during the production process of crab marinated in soy sauce, potential microbial hazards, potential contamination routes and effective critical control points. Crab and soy sauce samples were obtained from six different manufacturing plants at different stages, and their microbiological content was comprehensively assessed by quantitative and qualitative analyses. The results revealed the following: (1) the final products contained 4.0 log colony-forming units (CFU) g -1 aerobic plate counts (APCs) and 1.1 log CFU g -1 coliforms, which may have been introduced from the raw materials (the level of APCs in raw crab and soy sauce mixed with other ingredients was 3.8 log CFU g -1 and 4.0 log CFU mL -1 respectively); (2) marination of crab in soy sauce may allow cross-contamination by coliforms; (3) only Bacillus cereus and Staphylococcus aureus were qualitatively detected in samples at different stages of manufacture (detection rate of 28 and 5.6% respectively), and these bacteria may impact the microbiological quality and safety of crab marinated in soy sauce; and (4) bacterial counts were either maintained or increased during the manufacturing process (suggesting that no particular step can be targeted to reduce bacterial counts). Proper management of raw materials and the marination process are effective critical control points, and alternative interventions may be needed to control bacterial quantity. The results provide important basic information about the production of crab marinated in soy sauce and may facilitate effective implementation of sanitary management practices in related industries and research fields. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  12. Marines in the Boxer Rebellion as a Model for Current Marine Corps Operations

    Science.gov (United States)

    2016-06-10

    O’Bannon received the Mameluke sword as a gift from Hamut, the same style sword Marine officers carry to this day.9 While the Barbary Wars would...disaster response operations in Indonesia, Bangladesh, Burma, Philippines, Haiti, Pakistan , Japan, Liberia, Senegal, Solomon Islands, Taiwan, and...Military Institute. Parents and grandparents of Marine officers in the first half of the twentieth century were at times veterans of the Confederacy

  13. Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

    Science.gov (United States)

    Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

  14. Using Integrated Environmental Modeling to Automate a Process-Based Quantitative Microbial Risk Assessment (presentation)

    Science.gov (United States)

    Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and...

  15. Model Based Control of Single-Phase Marine Cooling Systems

    DEFF Research Database (Denmark)

    Hansen, Michael

    2014-01-01

    these systems. Traditionally, control for this type of cooling system has been limited to open-loop control of pumps combined with a couple of local PID controllers for bypass valves to keep critical temperatures within design limits. This research considers improvements in a retrofit framework to the control...... linearization, an H∞-control design is applied to the resulting linear system. Disturbance rejection capabilities and robustness of performance for this control design methodology is compared to a baseline design derived from classical control theory. This shows promising results for the nonlinear robust design......This thesis is concerned with the problem of designing model-based control for a class of single-phase marine cooling systems. While this type of cooling system has been in existence for several decades, it is only recently that energy efficiency has become a focus point in the design and operation...

  16. Marine microbial L-asparaginase: Biochemistry, molecular approaches and applications in tumor therapy and in food industry.

    Science.gov (United States)

    Izadpanah Qeshmi, Fatemeh; Homaei, Ahmad; Fernandes, Pedro; Javadpour, Sedigheh

    2018-03-01

    The marine environment is a rich source of biological and chemical diversity. It covers more than 70% of the Earth's surface and features a wide diversity of habitats, often displaying extreme conditions, where marine organisms thrive, offering a vast pool for microorganisms and enzymes. Given the dissimilarity between marine and terrestrial habitats, enzymes and microorganisms, either novel or with different and appealing features as compared to terrestrial counterparts, may be identified and isolated. L-asparaginase (E.C. 3.5.1.1), is among the relevant enzymes that can be obtained from marine sources. This amidohydrolase acts on L-asparagine and produce L-aspartate and ammonia, accordingly it has an acknowledged chemotherapeutic application, namely in acute lymphoblastic leukemia. Moreover, L-asparaginase is also of interest in the food industry as it prevents acrylamide formation. Terrestrial organisms have been largely tapped for L-asparaginases, but most failed to comply with criteria for practical applications, whereas marine sources have only been marginally screened. This work provides an overview on the relevant features of this enzyme and the framework for its application, with a clear emphasis on the use of L-asparaginase from marine sources. The review envisages to highlight the unique properties of marine L-asparaginases that could make them good candidates for medical applications and industries, especially in food safety. Copyright © 2018 Elsevier GmbH. All rights reserved.

  17. Comparison of multivariate microbial datasets with the Shannon index: An example using enzyme activity from diverse marine environments

    DEFF Research Database (Denmark)

    Steen, Andrew; Ziervogel, K.; Arnosti, C.

    2010-01-01

    Heterotrophic microbial communities contain substantial functional diversity, so studies of community function often generate multivariate data sets. Techniques for data reduction and analysis can help elucidate qualitative differences among sites from multivariate data sets that may be difficult...

  18. Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model.

    Science.gov (United States)

    Miki, Takeshi; Ushio, Masayuki; Fukui, Shin; Kondoh, Michio

    2010-08-10

    Theory and empirical evidence suggest that plant-soil feedback (PSF) determines the structure of a plant community and nutrient cycling in terrestrial ecosystems. The plant community alters the nutrient pool size in soil by affecting litter decomposition processes, which in turn shapes the plant community, forming a PSF system. However, the role of microbial decomposers in PSF function is often overlooked, and it remains unclear whether decomposers reinforce or weaken litter-mediated plant control over nutrient cycling. Here, we present a theoretical model incorporating the functional diversity of both plants and microbial decomposers. Two fundamental microbial processes are included that control nutrient mineralization from plant litter: (i) assimilation of mineralized nutrient into the microbial biomass (microbial immobilization), and (ii) release of the microbial nutrients into the inorganic nutrient pool (net mineralization). With this model, we show that microbial diversity may act as a buffer that weakens plant control over the soil nutrient pool, reversing the sign of PSF from positive to negative and facilitating plant coexistence. This is explained by the decoupling of litter decomposability and nutrient pool size arising from a flexible change in the microbial community composition and decomposition processes in response to variations in plant litter decomposability. Our results suggest that the microbial community plays a central role in PSF function and the plant community structure. Furthermore, the results strongly imply that the plant-centered view of nutrient cycling should be changed to a plant-microbe-soil feedback system, by incorporating the community ecology of microbial decomposers and their functional diversity.

  19. Application of human and animal viral microbial source tracking tools in fresh and marine waters from five different geographical areas.

    Science.gov (United States)

    Rusiñol, Marta; Fernandez-Cassi, Xavier; Hundesa, Ayalkibet; Vieira, Carmen; Kern, Anita; Eriksson, Irene; Ziros, Panos; Kay, David; Miagostovich, Marize; Vargha, Marta; Allard, Annika; Vantarakis, Apostolos; Wyn-Jones, Peter; Bofill-Mas, Sílvia; Girones, Rosina

    2014-08-01

    Integrated river basin management planning to mitigate the impacts of economic, demographic and climate change is an important issue for the future protection of water resources. Identifying sources of microbial contamination via the emerging science of Microbial Source Tracking (MST) plays a key role in risk assessment and the design of remediation strategies. Following an 18-month surveillance program within the EU-FP7-funded VIROCLIME project, specific MST tools were used to assess human markers such as adenoviruses (HAdV) and JC polyomaviruses (JCPyV) and porcine and bovine markers such as porcine adenoviruses (PAdV) and bovine polyomaviruses (BPyV) via quantification with real-time PCR to analyze surface water collected from five sites within different climatic zones: the Negro River (Brazil), Glafkos River (Greece), Tisza River (Hungary), Llobregat River (Spain) and Umeälven River (Sweden). The utility of the viral MST tools and the prevalence and abundance of specific human and animal viruses in the five river catchments and adjacent seawater, which is impacted by riverine contributions from the upstream catchments, were examined. In areas where no sanitation systems have been implemented, sewage can directly enter surface waters, and river water exhibited high viral loads; HAdV and JCPyV could be detected at mean concentrations of 10(5) and 10(4) Genome Copies/Liter (GC/L), respectively. In general, river water samples upstream of urban discharges presented lower human viral loads than downstream sampling sites, and those differences appeared to increase with urban populations but decrease in response to high river flow, as the elevated river water volume dilutes microbial loads. During dry seasons, river water flow decreases dramatically, and secondary effluents can represent the bulk of the riverine discharge. We also observed that ice cover that formed over the river during the winter in the studied areas in North Europe could preserve viral stability

  20. A Mathematical Model of Marine Diesel Engine Speed Control System

    Science.gov (United States)

    Sinha, Rajendra Prasad; Balaji, Rajoo

    2018-02-01

    Diesel engine is inherently an unstable machine and requires a reliable control system to regulate its speed for safe and efficient operation. Also, the diesel engine may operate at fixed or variable speeds depending upon user's needs and accordingly the speed control system should have essential features to fulfil these requirements. This paper proposes a mathematical model of a marine diesel engine speed control system with droop governing function. The mathematical model includes static and dynamic characteristics of the control loop components. Model of static characteristic of the rotating fly weights speed sensing element provides an insight into the speed droop features of the speed controller. Because of big size and large time delay, the turbo charged diesel engine is represented as a first order system or sometimes even simplified to a pure integrator with constant gain which is considered acceptable in control literature. The proposed model is mathematically less complex and quick to use for preliminary analysis of the diesel engine speed controller performance.

  1. Optimisation of Marine Boilers using Model-based Multivariable Control

    OpenAIRE

    Solberg, Brian

    2008-01-01

    Traditionally, marine boilers have been controlled using classical single loop controllers. To optimise marine boiler performance, reduce new installation time and minimise the physical dimensions of these large steel constructions, a more comprehensive and coherent control strategy is needed. This research deals with the application of advanced control to a specific class of marine boilers combining well-known design methods for multivariable systems.This thesis presents contributions for mo...

  2. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

    Science.gov (United States)

    Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

    2016-01-01

    We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can

  3. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.

    Science.gov (United States)

    Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

    2016-01-01

    We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can

  4. Metabolic network modeling of microbial interactions in natural and engineered environmental systems

    Directory of Open Access Journals (Sweden)

    Octavio ePerez-Garcia

    2016-05-01

    Full Text Available We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA, experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e. i lumped networks, ii compartment per guild networks, iii bi-level optimization simulations and iv dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial

  5. Seasonality in ocean microbial communities.

    Science.gov (United States)

    Giovannoni, Stephen J; Vergin, Kevin L

    2012-02-10

    Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

  6. The worm has turned--microbial virulence modeled in Caenorhabditis elegans.

    Science.gov (United States)

    Sifri, Costi D; Begun, Jakob; Ausubel, Frederick M

    2005-03-01

    The nematode Caenorhabditis elegans is emerging as a facile and economical model host for the study of evolutionarily conserved mechanisms of microbial pathogenesis and innate immunity. A rapidly growing number of human and animal microbial pathogens have been shown to injure and kill nematodes. In many cases, microbial genes known to be important for full virulence in mammalian models have been shown to be similarly required for maximum pathogenicity in nematodes. C. elegans has been used in mutation-based screening systems to identify novel virulence-related microbial genes and immune-related host genes, many of which have been validated in mammalian models of disease. C. elegans-based pathogenesis systems hold the potential to simultaneously explore the molecular genetic determinants of both pathogen virulence and host defense.

  7. The Smithsonian-led Marine Global Earth Observatory (MarineGEO): Proposed Model for a Collaborative Network Linking Marine Biodiversity to Ecosystem Processes

    Science.gov (United States)

    Duffy, J. E.

    2016-02-01

    Biodiversity - the variety of functional types of organisms - is the engine of marine ecosystem processes, including productivity, nutrient cycling, and carbon sequestration. Biodiversity remains a black box in much of ocean science, despite wide recognition that effectively managing human interactions with marine ecosystems requires understanding both structure and functional consequences of biodiversity. Moreover, the inherent complexity of biological systems puts a premium on data-rich, comparative approaches, which are best met via collaborative networks. The Smithsonian Institution's MarineGEO program links a growing network of partners conducting parallel, comparative research to understand change in marine biodiversity and ecosystems, natural and anthropogenic drivers of that change, and the ecological processes mediating it. The focus is on nearshore, seabed-associated systems where biodiversity and human population are concentrated and interact most, yet which fall through the cracks of existing ocean observing programs. MarineGEO offers a standardized toolbox of research modules that efficiently capture key elements of biological diversity and its importance in ecological processes across a range of habitats. The toolbox integrates high-tech (DNA-based, imaging) and low-tech protocols (diver surveys, rapid assays of consumer activity) adaptable to differing institutional capacity and resources. The model for long-term sustainability involves leveraging in-kind support among partners, adoption of best practices wherever possible, engagement of students and citizen scientists, and benefits of training, networking, and global relevance as incentives for participation. Here I highlight several MarineGEO comparative research projects demonstrating the value of standardized, scalable assays and parallel experiments for measuring fish and invertebrate diversity, recruitment, benthic herbivory and generalist predation, decomposition, and carbon sequestration. Key

  8. GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Radhakrishnan Mahadevan

    2012-10-01

    With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  9. Modelling microbial exchanges between forms of soil nitrogen in contrasting ecosystems

    Science.gov (United States)

    Pansu, M.; Machado, D.; Bottner, P.; Sarmiento, L.

    2014-02-01

    Although nitrogen (N) is often combined with carbon (C) in organic molecules, C passes from the air to the soil through plant photosynthesis, whereas N passes from the soil to plants through a chain of microbial conversions. However, dynamic models do not fully consider the microorganisms at the centre of exchange processes between organic and mineral forms of N. This study monitored the transfer of 14C and 15N between plant materials, microorganisms, humified compartments, and inorganic forms in six very different ecosystems along an altitudinal transect. The microbial conversions of the 15N forms appear to be strongly linked to the previously modelled C cycle, and the same equations and parameters can be used to model both C and N cycles. The only difference is in the modelling of the flows between microbial and inorganic forms. The processes of mineralization and immobilization of N appear to be regulated by a two-way microbial exchange depending on the C : N ratios of microorganisms and available substrates. The MOMOS (Modelling of Organic Matter of Soils) model has already been validated for the C cycle and also appears to be valid for the prediction of microbial transformations of N forms. This study shows that the hypothesis of microbial homeostasis can give robust predictions at global scale. However, the microbial populations did not appear to always be independent of the external constraints. At some altitudes their C : N ratio could be better modelled as decreasing during incubation and increasing with increasing C storage in cold conditions. The ratio of potentially mineralizable-15N/inorganic-15N and the 15N stock in the plant debris and the microorganisms was modelled as increasing with altitude, whereas the 15N storage in stable humus was modelled as decreasing with altitude. This predicts that there is a risk that mineralization of organic reserves in cold areas may increase global warming.

  10. A fermented meat model system for studies of microbial aroma formation

    DEFF Research Database (Denmark)

    Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

    2003-01-01

    A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter...... and model, fast-acidified samples had a high content of ketones, sulphides and methyl-branched acids, whereas slowly acidified samples had the highest content of methyl-branched alcohols, aldehydes, their ethyl esters, phenylacetaldehyde and methional. Furthermore, model repeatability with respect to p......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage....

  11. OCEANFILMS-2: Representing coadsorption of saccharides in marine films and potential impacts on modeled marine aerosol chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Burrows, Susannah M. [Atmospheric Science and Global Change Division, Pacific Northwest National Laboratory, Richland Washington USA; Gobrogge, Eric [Department of Chemistry and Biochemistry, Montana State University, Bozeman Montana USA; Fu, Li [Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington USA; Link, Katie [Department of Chemistry and Biochemistry, Montana State University, Bozeman Montana USA; Elliott, Scott M. [Climate, Ocean, and Sea Ice Modelling Group, Los Alamos National Laboratory, Los Alamos New Mexico USA; Wang, Hongfei [Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington USA; Walker, Rob [Department of Chemistry and Biochemistry, Montana State University, Bozeman Montana USA

    2016-08-10

    Here we show that the addition of chemical interactions of soluble polysaccharides with a surfactant monolayer improves agreement of modeled sea spray chemistry with observed marine aerosol chemistry. In particular, the fraction of hydroxyl functional groups in modeled sea spray organic matter is increased, improving agreement with FTIR observations of marine aerosol composition. The overall organic fraction of submicron sea spray also increases, allowing organic mass fractions in the range 0.5 – 0.7 for submicron sea spray particles over highly active phytoplankton blooms. We show results from Sum Frequency Generation (SFG) experiments that support the modeling approach, by demonstrating that soluble polysaccharides can strongly adsorb to a lipid monolayer via columbic interactions under appropriate conditions.

  12. BiomeNet: a Bayesian model for inference of metabolic divergence among microbial communities.

    OpenAIRE

    Mahdi Shafiei; Katherine A Dunn; Hugh Chipman; Hong Gu; Joseph P Bielawski

    2014-01-01

    Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic subnetworks among microbial communities. To infer the structure of community-level metabolic interactions...

  13. Influence of Sea Ice on Arctic Marine Sulfur Biogeochemistry in the Community Climate System Model

    Energy Technology Data Exchange (ETDEWEB)

    Deal, Clara [Univ. of Alaska, Fairbanks, AL (United States); Jin, Meibing [Univ. of Alaska, Fairbanks, AL (United States)

    2013-06-30

    Global climate models (GCMs) have not effectively considered how responses of arctic marine ecosystems to a warming climate will influence the global climate system. A key response of arctic marine ecosystems that may substantially influence energy exchange in the Arctic is a change in dimethylsulfide (DMS) emissions, because DMS emissions influence cloud albedo. This response is closely tied to sea ice through its impacts on marine ecosystem carbon and sulfur cycling, and the ice-albedo feedback implicated in accelerated arctic warming. To reduce the uncertainty in predictions from coupled climate simulations, important model components of the climate system, such as feedbacks between arctic marine biogeochemistry and climate, need to be reasonably and realistically modeled. This research first involved model development to improve the representation of marine sulfur biogeochemistry simulations to understand/diagnose the control of sea-ice-related processes on the variability of DMS dynamics. This study will help build GCM predictions that quantify the relative current and possible future influences of arctic marine ecosystems on the global climate system. Our overall research objective was to improve arctic marine biogeochemistry in the Community Climate System Model (CCSM, now CESM). Working closely with the Climate Ocean Sea Ice Model (COSIM) team at Los Alamos National Laboratory (LANL), we added 1 sea-ice algae and arctic DMS production and related biogeochemistry to the global Parallel Ocean Program model (POP) coupled to the LANL sea ice model (CICE). Both CICE and POP are core components of CESM. Our specific research objectives were: 1) Develop a state-of-the-art ice-ocean DMS model for application in climate models, using observations to constrain the most crucial parameters; 2) Improve the global marine sulfur model used in CESM by including DMS biogeochemistry in the Arctic; and 3) Assess how sea ice influences DMS dynamics in the arctic marine

  14. A fermented meat model system for studies of microbial aroma formation

    DEFF Research Database (Denmark)

    Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

    2003-01-01

    A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starte......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage.......A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter...... cultures Pediococcus pentosaceus and Staphylococcus xylosus. Volatiles were collected and analysed by dynamic headspace sampling and GC MS. The analysis was primarily focused on volatiles arising from amino acid degradation and a total of 24 compounds, of which 19 were quantified, were used...

  15. Validation of the marine vegetation model in Forsmark. SFR-Site Forsmark

    International Nuclear Information System (INIS)

    Aquilonius, Karin; Qvarfordt, Susanne; Borgiel, Micke

    2011-04-01

    A regression model implemented in GIS of the marine vegetation in Forsmark were developed by SKB /Aquilonius 2010/ based on field investigations and video surveys /Fredriksson 2005/ and from correlations of field data and physical properties /Carlen et al. 2007/. The marine vegetation model describes distribution and biomasses of the marine vegetation and is used as input data in the dose modeling within the safety assessments performed by the SKB. In this study the predictive performance of the vegetation model in the less examined parts of the marine area in Forsmark is evaluated. In general, the vegetation model works very well in predicting absence of biomass, except for Red algae. In total and for Fucus sp., the model also predicts the observed biomass fairly well. However, for phanerogams, Chara sp., filamentous algae and red algae the vegetation model works less well in predicting biomass

  16. Validation of the marine vegetation model in Forsmark. SFR-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Aquilonius, Karin (Studsvik Nuclear AB (Sweden)); Qvarfordt, Susanne; Borgiel, Micke (Sveriges Vattenekologer AB (Sweden))

    2011-04-15

    A regression model implemented in GIS of the marine vegetation in Forsmark were developed by SKB /Aquilonius 2010/ based on field investigations and video surveys /Fredriksson 2005/ and from correlations of field data and physical properties /Carlen et al. 2007/. The marine vegetation model describes distribution and biomasses of the marine vegetation and is used as input data in the dose modeling within the safety assessments performed by the SKB. In this study the predictive performance of the vegetation model in the less examined parts of the marine area in Forsmark is evaluated. In general, the vegetation model works very well in predicting absence of biomass, except for Red algae. In total and for Fucus sp., the model also predicts the observed biomass fairly well. However, for phanerogams, Chara sp., filamentous algae and red algae the vegetation model works less well in predicting biomass

  17. Integration of protein extraction with a stream of byproducts from marine macroalgae: A model forms the basis for marine bioeconomy.

    Science.gov (United States)

    Gajaria, Tejal K; Suthar, Poornima; Baghel, Ravi S; Balar, Nikunj B; Sharnagat, Preeti; Mantri, Vaibhav A; Reddy, C R K

    2017-11-01

    The present study describes an advanced biorefinery model for marine macroalgae that assumes significant importance in the context of marine bio-economy. The method investigated in this study integrates the extraction of crude proteins with recovery of minerals rich sap, lipids, ulvan and cellulose from fresh biomass of Ulva lactuca. The protein content extracted was 11±2.12% on dry weight basis with recovery efficiency of 68.75±4.01%. The amino acid composition of crude protein fraction showed iso-leucine as the most abundant amino acid with 16.51±0.03% followed by histidine, arginine, tyrosine, serine, aspartic acid, threonine, phenyl alanine, leucine, alanine, lysine, glycine and glutamic acid (0.22±0.24%). The digestibility of protein was as high as 85.86±5.92% indicating its suitability for use in food supplements. The protein production with co-recovery of other products would not only result in effective utilisation marine macroalgal resources but also forms the basis for marine bio-economy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Assessment of the performance of SMFCs in the bioremediation of PAHs in contaminated marine sediments under different redox conditions and analysis of the associated microbial communities

    KAUST Repository

    Hamdan, Hamdan Z.

    2016-10-09

    The biodegradation of naphthalene, 2-methylnaphthalene and phenanthrene was evaluated in marine sediment microbial fuel cells (SMFCs) under different biodegradation conditions, including sulfate reduction as a major biodegradation pathway, employment of anode as terminal electron acceptor (TEA) under inhibited sulfate reducing bacteria activity, and combined sulfate and anode usage as electron acceptors. A significant removal of naphthalene and 2-methylnaphthalene was observed at early stages of incubation in all treatments and was attributed to their high volatility. In the case of phenanthrene, a significant removal (93.83 ± 1.68%) was measured in the closed circuit SMFCs with the anode acting as the main TEA and under combined anode and sulfate reduction conditions (88.51 ± 1.3%). A much lower removal (40.37 ± 3.24%) was achieved in the open circuit SMFCs operating with sulfate reduction as a major biodegradation pathway. Analysis of the anodic bacterial community using 16S rRNA gene pyrosequencing revealed the enrichment of genera with potential exoelectrogenic capability, namely Geoalkalibacter and Desulfuromonas, on the anode of the closed circuit SMFCs under inhibited SRB activity, while they were not detected on the anode of open circuit SMFCs. These results demonstrate the role of the anode in enhancing PAHs biodegradation in contaminated marine sediments and suggest a higher system efficiency in the absence of competition between microbial redox processes (under SRB inhibition), namely due to the anode enrichment with exoelectrogenic bacteria, which is a more energetically favorable mechanism for PAHs oxidation than sulfate.

  19. Effects of deposition of heavy-metal-polluted harbor mud on microbial diversity and metal resistance in sandy marine sediments

    DEFF Research Database (Denmark)

    Toes, Ann-Charlotte M; Finke, Niko; Kuenen, J Gijs

    2008-01-01

    Deposition of dredged harbor sediments in relatively undisturbed ecosystems is often considered a viable option for confinement of pollutants and possible natural attenuation. This study investigated the effects of deposition of heavy-metal-polluted sludge on the microbial diversity of sandy sedi...

  20. Effects of Deposition of Heavy-Metal-Polluted Harbor Mud on Microbial Diversity and Metal Resistance in Sandy Marine Sediments

    NARCIS (Netherlands)

    Toes, A.C.M.; Finke, N.; Kuenen, J.G.; Muyzer, G.

    2008-01-01

    Deposition of dredged harbor sediments in relatively undisturbed ecosystems is often considered a viable option for confinement of pollutants and possible natural attenuation. This study investigated the effects of deposition of heavy-metal-polluted sludge on the microbial diversity of sandy

  1. Dynamic modeling of environmental risk associated with drilling discharges to marine sediments.

    Science.gov (United States)

    Durgut, İsmail; Rye, Henrik; Reed, Mark; Smit, Mathijs G D; Ditlevsen, May Kristin

    2015-10-15

    Drilling discharges are complex mixtures of base-fluids, chemicals and particulates, and may, after discharge to the marine environment, result in adverse effects on benthic communities. A numerical model was developed to estimate the fate of drilling discharges in the marine environment, and associated environmental risks. Environmental risk from deposited drilling waste in marine sediments is generally caused by four types of stressors: oxygen depletion, toxicity, burial and change of grain size. In order to properly model these stressors, natural burial, biodegradation and bioturbation processes were also included. Diagenetic equations provide the basis for quantifying environmental risk. These equations are solved numerically by an implicit-central differencing scheme. The sediment model described here is, together with a fate and risk model focusing on the water column, implemented in the DREAM and OSCAR models, both available within the Marine Environmental Modeling Workbench (MEMW) at SINTEF in Trondheim, Norway. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. CONCEPTS, MODELS AND IMPLEMENTATION OF THE MARINE SPATIAL DATA INFRASTRUCTURE IN GERMANY (MDI-DE

    Directory of Open Access Journals (Sweden)

    C. Rüh

    2012-07-01

    Full Text Available In Germany currently the development of a marine data infrastructure takes place with the aim of merging information concerning the fields coastal engineering, hydrography and surveying, protection of the marine environment, maritime conservation, regional planning and coastal research. This undertaking is embedded in a series of regulations and developments on many administrative levels from which specifications and courses of action derive. To set up a conceptual framework for the marine data infrastructure (MDI-DE scientists at the Professorship for Geodesy and Geoinformatics at Rostock University are building a reference model, evaluating meta-information systems and developing models to support common workflows in marine applications. The reference model for the marine spatial data infrastructure of Germany (MDI-DE is the guideline for all developments inside this infrastructure. Because the undertaking is embedded in a series of regulations and developments this paper illustrates an approach on modelling a scenario for the Marine Strategy Framework Directive (MSFD using the Unified Modelling Language (UML. Evaluating how other countries built their marine spatial infrastructures is of main importance, to learn where obstacles are and errors are likely to occur. To be able to look at other initiatives from a neutral point of view it is necessary to construct a framework for evaluation of marine spatial data infrastructures. Spatial data infrastructure assessment approaches were used as bases and were expanded to meet the requirements of the marine domain. As an international case-study this paper will look at Canada's Marine Geospatial Data Infrastructure (MGDI, COINAtlantic and GeoPortal.

  3. Concepts, Models and Implementation of the Marine Spatial Data Infrastructure in Germany Mdi-De

    Science.gov (United States)

    Rüh, C.; Bill, R.

    2012-07-01

    In Germany currently the development of a marine data infrastructure takes place with the aim of merging information concerning the fields coastal engineering, hydrography and surveying, protection of the marine environment, maritime conservation, regional planning and coastal research. This undertaking is embedded in a series of regulations and developments on many administrative levels from which specifications and courses of action derive. To set up a conceptual framework for the marine data infrastructure (MDI-DE) scientists at the Professorship for Geodesy and Geoinformatics at Rostock University are building a reference model, evaluating meta-information systems and developing models to support common workflows in marine applications. The reference model for the marine spatial data infrastructure of Germany (MDI-DE) is the guideline for all developments inside this infrastructure. Because the undertaking is embedded in a series of regulations and developments this paper illustrates an approach on modelling a scenario for the Marine Strategy Framework Directive (MSFD) using the Unified Modelling Language (UML). Evaluating how other countries built their marine spatial infrastructures is of main importance, to learn where obstacles are and errors are likely to occur. To be able to look at other initiatives from a neutral point of view it is necessary to construct a framework for evaluation of marine spatial data infrastructures. Spatial data infrastructure assessment approaches were used as bases and were expanded to meet the requirements of the marine domain. As an international case-study this paper will look at Canada's Marine Geospatial Data Infrastructure (MGDI), COINAtlantic and GeoPortal.

  4. A spatio-temporal process data model for characterizing marine disasters

    International Nuclear Information System (INIS)

    Jiang, B; Gao, T; Zhang, X; Huang, X

    2014-01-01

    Marine disasters are a more prevalent problem in China than in many other countries. Based on the development of a status quo of China's marine disaster the space-time process model is used. The model uses the ocean's temperature field, salinity field, water density field, surface wind field, wave field and other four-dimensional spatio-temporal quantities. This paper studies that model in detail. This study aims at using the theory to provide support during marine disasters in an effort to prevent or decrease their frequency in the future

  5. Anisotropic mesh adaptation for marine ice-sheet modelling

    Science.gov (United States)

    Gillet-Chaulet, Fabien; Tavard, Laure; Merino, Nacho; Peyaud, Vincent; Brondex, Julien; Durand, Gael; Gagliardini, Olivier

    2017-04-01

    Improving forecasts of ice-sheets contribution to sea-level rise requires, amongst others, to correctly model the dynamics of the grounding line (GL), i.e. the line where the ice detaches from its underlying bed and goes afloat on the ocean. Many numerical studies, including the intercomparison exercises MISMIP and MISMIP3D, have shown that grid refinement in the GL vicinity is a key component to obtain reliable results. Improving model accuracy while maintaining the computational cost affordable has then been an important target for the development of marine icesheet models. Adaptive mesh refinement (AMR) is a method where the accuracy of the solution is controlled by spatially adapting the mesh size. It has become popular in models using the finite element method as they naturally deal with unstructured meshes, but block-structured AMR has also been successfully applied to model GL dynamics. The main difficulty with AMR is to find efficient and reliable estimators of the numerical error to control the mesh size. Here, we use the estimator proposed by Frey and Alauzet (2015). Based on the interpolation error, it has been found effective in practice to control the numerical error, and has some flexibility, such as its ability to combine metrics for different variables, that makes it attractive. Routines to compute the anisotropic metric defining the mesh size have been implemented in the finite element ice flow model Elmer/Ice (Gagliardini et al., 2013). The mesh adaptation is performed using the freely available library MMG (Dapogny et al., 2014) called from Elmer/Ice. Using a setup based on the inter-comparison exercise MISMIP+ (Asay-Davis et al., 2016), we study the accuracy of the solution when the mesh is adapted using various variables (ice thickness, velocity, basal drag, …). We show that combining these variables allows to reduce the number of mesh nodes by more than one order of magnitude, for the same numerical accuracy, when compared to uniform mesh

  6. Data-Driven Microbial Modeling for Soil Carbon Decomposition and Stabilization

    Science.gov (United States)

    Luo, Yiqi; Chen, Ji; Chen, Yizhao; Feng, Wenting

    2017-04-01

    Microorganisms have long been known to catalyze almost all the soil organic carbon (SOC) transformation processes (e.g., decomposition, stabilization, and mineralization). Representing microbial processes in Earth system models (ESMs) has the potential to improve projections of SOC dynamics. We have recently examined (1) relationships of microbial functions with environmental factors and (2) microbial regulations of decomposition and other key soil processes. According to three lines of evidence, we have developed a data-driven enzyme (DENZY) model to simulate soil microbial decomposition and stabilization. First, our meta-analysis of 64 published field studies showed that field experimental warming significantly increased soil microbial communities abundance, which is negatively correlated with the mean annual temperature. The negative correlation indicates that warming had stronger effects in colder than warmer regions. Second, we found that the SOC decomposition, especially the transfer between labile SOC and protected SOC, is nonlinearly regulated by soil texture parameters, such as sand and silt contents. Third, we conducted a global analysis of the C-degrading enzyme activities, soil respiration, and SOC content under N addition. Our results show that N addition has contrasting effects on cellulase (hydrolytic C-degrading enzymes) and ligninase (oxidative C-degrading enzymes) activities. N-enhanced cellulase activity contributes to the minor stimulation of soil respiration whereas N-induced repression on ligninase activity drives soil C sequestration. Our analysis links the microbial extracellular C-degrading enzymes to the SOC dynamics at ecosystem scales across scores of experimental sites around the world. It offers direct evidence that N-induced changes in microbial community and physiology play fundamental roles in controlling the soil C cycle. Built upon those three lines of empirical evidence, the DENZY model includes two enzyme pools and explicitly

  7. Applications of artificial neural networks for microbial water quality modeling

    International Nuclear Information System (INIS)

    Brion, G.M.; Lingireddy, S.

    2002-01-01

    There has been a significant shift in the recent past towards protecting chemical and microbial quality of source waters rather than developing advanced methods to treat heavily polluted water. The key to successful best management practices in protecting the source waters is to identify sources of non-point pollution and their collective impact on the quality of water at the intake. This article presents a few successful applications where artificial neural networks (ANN) have proven to be the useful mathematical tools in correlating the nonlinear relationships between routinely measured parameters (such as rainfall, turbidity, fecal coliforms etc.) and quality of source waters and/or nature of fecal sources. These applications include, prediction of peak concentrations of Giardia and Cryptosporidium, sorting of fecal sources (e.g. agricultural animals vs. urban animals), predicting relative ages of the runoff sources, identifying the potential for sewage contamination. The ability of ANNs to work with complex, inter-related multiparameter databases, and provide superior predictive power in non-linear relationships has been the key for their successful application to microbial water quality studies. (author)

  8. LINKING MICROBES TO CLIMATE: INCORPORATING MICROBIAL ACTIVITY INTO CLIMATE MODELS COLLOQUIUM

    Energy Technology Data Exchange (ETDEWEB)

    DeLong, Edward; Harwood, Caroline; Reid, Ann

    2011-01-01

    This report explains the connection between microbes and climate, discusses in general terms what modeling is and how it applied to climate, and discusses the need for knowledge in microbial physiology, evolution, and ecology to contribute to the determination of fluxes and rates in climate models. It recommends with a multi-pronged approach to address the gaps.

  9. Predicting microbial growth kinetics with the use of genetic circuit models

    NARCIS (Netherlands)

    Koutinas, M.; Kiparissides, A.; Lorenzo, de V.; Martins Dos Santos, V.A.P.; Pistikopoulos, E.N.; Mantalaris, A.

    2011-01-01

    A novel modeling approach for the description of bioprocesses is proposed, linking microbial growth kinetics to gene regulation. An example is given with the development and experimental validation of a dynamic mathematical model of the TOL plasmid of Pseudomonas putida mt-2, which is used for the

  10. Modelling microbial fuel cells with suspended cells and added electron transfer mediator

    NARCIS (Netherlands)

    Picoreanu, C.; Katuri, K.P.; Van Loosdrecht, M.C.M.; Head, I.M.; Scott, K.

    2009-01-01

    Derivation of a mathematical model for microbial fuel cells (MFC) with suspended biomass and added electron-transfer mediator is described. The model is based on mass balances for several dissolved chemical species such as substrate, oxidized mediator and reduced mediator. Biological, chemical and

  11. Kinetic models for detection of toxicity in a microbial fuel cell based biosensor

    NARCIS (Netherlands)

    Stein, N.E.; Keesman, K.J.; Hamelers, H.V.M.; Straten, van G.

    2011-01-01

    Currently available models describing microbial fuel cell (MFC) polarization curves, do not describe the effect of the presence of toxic components. A bioelectrochemical model combined with enzyme inhibition kinetics, that describes the polarization curve of an MFC-based biosensor, was modified to

  12. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulfidic marine sediments

    Energy Technology Data Exchange (ETDEWEB)

    Glass, DR. Jennifer [California Institute of Technology, Pasadena; Yu, DR. Hang [California Institute of Technology, Pasadena; Steele, Joshua [California Institute of Technology, Pasadena; Dawson, Katherine [California Institute of Technology, Pasadena; Sun, S [University of California, San Diego; Chourey, Karuna [ORNL; Hettich, Robert {Bob} L [ORNL; Orphan, V [California Institute of Technology, Pasadena

    2014-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyze important biogeochemical reactions. In anoxic methane- and sulfide-rich environments, microbes may have unique adaptations for metal acquisition and utilization due to decreased bioavailability as a result of metal sulfide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulfidic (>1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5,600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalyzing anaerobic oxidation of methane utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrotolerant microorganisms. Finally, our data suggest that chemical speciation of metals in highly sulfidic porewaters may exert a stronger influence on microbial bioavailability than total concentration

  13. A global census of marine microbes

    Digital Repository Service at National Institute of Oceanography (India)

    Amaral-Zettler, L.; Artigas, L.F.; Baross, J.; LokaBharathi, P.A; Boetius, A; Chandramohan, D.; Herndl, G.; Kogure, K.; Neal, P.; Pedros-Alio, C.; Ramette, A; Schouten, S.; Stal, L.; Thessen, A; De Leeuw, J.; Sogin, M.

    In this chapter we provide a brief history of what is known about marine microbial diversity, summarize our achievements in performing a global census of marine microbes, and reflect on the questions and priorities for the future of the marine...

  14. Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvania stream.

    Science.gov (United States)

    Hong, Eun-Mi; Shelton, Daniel; Pachepsky, Yakov A; Nam, Won-Ho; Coppock, Cary; Muirhead, Richard

    2017-02-01

    Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four years to adequately evaluate the quality of water intended for produce irrigation. The objective of this work was to evaluate the effect of interannual weather variability on surface water microbial quality. We used the Soil and Water Assessment Tool model to simulate E. coli concentrations in the Little Cove Creek; this is a perennial creek located in an agricultural watershed in south-eastern Pennsylvania. The model performance was evaluated using the US FDA regulatory microbial water quality metrics of geometric mean (GM) and the statistical threshold value (STV). Using the 90-year time series of weather observations, we simulated and randomly sampled the time series of E. coli concentrations. We found that weather conditions of a specific year may strongly affect the evaluation of microbial quality and that the long-term assessment of microbial water quality may be quite different from the evaluation based on short-term observations. The variations in microbial concentrations and water quality metrics were affected by location, wetness of the hydrological years, and seasonality, with 15.7-70.1% of samples exceeding the regulatory threshold. The results of this work demonstrate the value of using modeling to design and evaluate monitoring protocols to assess the microbial quality of water used for produce irrigation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Science.gov (United States)

    He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. David; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

    2015-01-01

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  16. Shore-based Path Planning for Marine Vehicles Using a Model of Ocean Currents

    Data.gov (United States)

    National Aeronautics and Space Administration — Develop path planning methods that incorporate an approximate model of ocean currents in path planning for a range of autonomous marine vehicles such as surface...

  17. Validation of the United States Marine Corps Qualified Candidate Population Model

    National Research Council Canada - National Science Library

    Hallahan, William

    2003-01-01

    This thesis attempts to verify, validate, and then expand a model of the population of college students that may be qualified and interested in seeking a commission in the United States Marine Corps...

  18. Scour around Support Structures of Scaled Model Marine Hydrokinetic Devices

    Science.gov (United States)

    Volpe, M. A.; Beninati, M. L.; Krane, M.; Fontaine, A.

    2013-12-01

    Experiments are presented to explore scour due to flows around support structures of marine hydrokinetic (MHK) devices. Three related studies were performed to understand how submergence, scour condition, and the presence of an MHK device impact scour around the support structure (cylinder). The first study focuses on clear-water scour conditions for a cylinder of varying submergence: surface-piercing and fully submerged. The second study centers on three separate scour conditions (clear-water, transitional and live-bed) around the fully submerged cylinder. Lastly, the third study emphasizes the impact of an MHK turbine on scour around the support structure, in live-bed conditions. Small-scale laboratory testing of model devices can be used to help predict the behavior of MHK devices at full-scale. Extensive studies have been performed on single cylinders, modeling bridge piers, though few have focused on fully submerged structures. Many of the devices being used to harness marine hydrokinetic energy are fully submerged in the flow. Additionally, scour hole dimensions and scour rates have not been addressed. Thus, these three studies address the effect of structure blockage/drag, and the ambient scour conditions on scour around the support structure. The experiments were performed in the small-scale testing platform in the hydraulic flume facility (9.8 m long, 1.2 m wide and 0.4 m deep) at Bucknell University. The support structure diameter (D = 2.54 cm) was held constant for all tests. The submerged cylinder (l/D = 5) and sediment size (d50 = 790 microns) were held constant for all three studies. The MHK device (Dturbine = 10.2 cm) is a two-bladed horizontal axis turbine and the rotating shaft is friction-loaded using a metal brush motor. For each study, bed form topology was measured after a three-hour time interval using a traversing two-dimensional bed profiler. During the experiments, scour hole depth measurements at the front face of the support structure

  19. Comparison of Two Mechanistic Microbial Growth Models to Estimate Shelf Life of Perishable Food Package under Dynamic Temperature Conditions

    Directory of Open Access Journals (Sweden)

    Dong Sun Lee

    2014-01-01

    Full Text Available Two mechanistic microbial growth models (Huang’s model and model of Baranyi and Roberts given in differential and integrated equation forms were compared in predicting the microbial growth and shelf life under dynamic temperature storage and distribution conditions. Literatures consistently reporting the microbial growth data under constant and changing temperature conditions were selected to obtain the primary model parameters, set up the secondary models, and apply them to predict the microbial growth and shelf life under fluctuating temperatures. When evaluated by general estimation behavior, bias factor, accuracy factor, and root-mean-square error, Huang’s model was comparable to Baranyi and Roberts’ model in the capability to estimate microbial growth under dynamic temperature conditions. Its simple form of single differential equation incorporating directly the growth rate and lag time may work as an advantage to be used in online shelf life estimation by using the electronic device.

  20. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.

    Science.gov (United States)

    Hurwitz, Bonnie L; Westveld, Anton H; Brum, Jennifer R; Sullivan, Matthew B

    2014-07-22

    Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes). Although protein clustering techniques provide a significant advance by helping organize this unknown metagenomic sequence space, they typically use only ∼75% of the data and rely on assembly methods not yet tuned for naturally occurring sequence variation. Here, we introduce an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure. Application to 32 viromes from the Pacific Ocean Virome dataset identified clusters of samples broadly delineated by photic zone and revealed that geographic region, depth, and proximity to shore were significant predictors of community structure. Within subsets of this dataset, depth, season, and oxygen concentration were significant drivers of viral community structure at a single open ocean station, whereas variability along onshore-offshore transects was driven by oxygen concentration in an area with an oxygen minimum zone and not depth or proximity to shore, as might be expected. Together these results demonstrate that this highly scalable approach using complete metagenomic network-based comparisons can both test and generate hypotheses for ecological investigation of viral and microbial communities in nature.

  1. Converted waves in shallow marine environments : Modelling and field experiments

    NARCIS (Netherlands)

    El Allouche, N.

    2011-01-01

    The shallow marine subsurface is explored for various engineering purposes e.g. constructing installations and platforms, laying pipelines and dredging for sand. Knowledge of the soil properties is essential to minimize the risks involved with these offshore activities. Energy resources in the form

  2. Preparation, characterization, and microbial degradation of specifically radiolabeled [14C]lignocelluloses from marine and fresh water macrophytes

    International Nuclear Information System (INIS)

    Benner, R.; Maccubbin, A.E.; Hodson, R.E.

    1984-01-01

    Specifically radiolabeled [ 14 C-lignin]lignocelluloses were prepared from the aquatic macrophytes Spartina alterniflora, Juncus roemerianus, Rhizophora mangle, and Carex walteriana by using [ 14 C]phenylalanine, [ 14 C]tyrosine, and [ 14 C]cinnamic acid as precursors. Specifically radiolabeled [ 14 C-polysaccharide]lignocelluloses were prepared by using [ 14 C]glucose as precursor. The rates of microbial degradation varied among [ 14 C-lignin]lignocelluloses labeled with different lignin precursors within the same plant species. In herbaceous plants, significant amounts (8 to 24%) of radioactivity from [ 14 C]phenylalanine and [ 14 C]tyrosine were found associated with protein. Microbial degradation of radiolabeled protein resulted in overestimation of lignin degradation rates in lignocelluloses derived from herbaceous aquatic plants. Other differences in degradation rates among [ 14 C-lignin]lignocelluloses from the same plant species were attributable to differences in the amount of label being associated with ester-linked subunits of peripheral lignin. After acid hydrolysis of [ 14 C-polysaccharide]lignocelluloses, radioactivity was detected in several sugars, although most of the radioactivity was distributed between glucose and xylose. After 576 h of incubation with salt marsh sediments, 38% of the polysaccharide component and between 6 and 16% of the lignin component (depending on the precursor) of J. roemerianus lignocellulose was mineralized to 14 CO 2 ; during the same incubation period, 30% of the polysaccharide component and between 12 and 18% of the lignin component of S. alterniflora lignocellulose was mineralized

  3. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

    Energy Technology Data Exchange (ETDEWEB)

    Glass, DR. Jennifer [California Institute of Technology, Pasadena; Yu, DR. Hang [California Institute of Technology, Pasadena; Steele, Joshua [California Institute of Technology, Pasadena; Dawson, Katherine [California Institute of Technology, Pasadena; Sun, S [University of California, San Diego; Chourey, Karuna [ORNL; Pan, Chongle [ORNL; Hettich, Robert {Bob} L [ORNL; Orphan, V [California Institute of Technology, Pasadena

    2013-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphiderich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulphidic (> 1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5 270 nM), cobalt (0.5 6 nM), molybdenum (10 5600 nM) and tungsten (0.3 8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.

  4. Marine geophysics. New global marine gravity model from CryoSat-2 and Jason-1 reveals buried tectonic structure.

    Science.gov (United States)

    Sandwell, David T; Müller, R Dietmar; Smith, Walter H F; Garcia, Emmanuel; Francis, Richard

    2014-10-03

    Gravity models are powerful tools for mapping tectonic structures, especially in the deep ocean basins where the topography remains unmapped by ships or is buried by thick sediment. We combined new radar altimeter measurements from satellites CryoSat-2 and Jason-1 with existing data to construct a global marine gravity model that is two times more accurate than previous models. We found an extinct spreading ridge in the Gulf of Mexico, a major propagating rift in the South Atlantic Ocean, abyssal hill fabric on slow-spreading ridges, and thousands of previously uncharted seamounts. These discoveries allow us to understand regional tectonic processes and highlight the importance of satellite-derived gravity models as one of the primary tools for the investigation of remote ocean basins. Copyright © 2014, American Association for the Advancement of Science.

  5. Mathematical modelling and research of passenger flows in marine passenger port

    Directory of Open Access Journals (Sweden)

    Vladimir A. Fetisov

    2017-03-01

    Full Text Available Modern passenger terminals are characterized by dynamic processes variability, diverse options consideration, taking into account the criteria of safety, reliability analysis and the continuous research of passenger processing. For any modern marine passenger terminal it is necessary to use the tool to simulate passenger flows. In this way it is possible to obtain the analytical information and use it for decision-making when solving the problem of the amount of personnel required for passenger services.in line with the original ship arrival schedule, to solve problems of forecasting groups at the terminal. Of particular relevance is the choice of the mathematical transport model and the practical conditions for the implementation of the model in the real terminal operation. In this article the analysis technique of simulation-based terminal services, provides a mathematical model of passenger movement inside the terminal. Also, the conditions of implementation of the transportation model during the operation of marine passenger terminal are examined. The object of the research is the marine Passenger Port of St. Petersburg "Marine Facade". The paper discusses advantages of using such systems and their introduction in the early stages of operation of the terminal. In addition, the conclusion about the effectiveness of such systems for the analysis of the correctness of internal space of the marine terminal. The study represents an example of analytical information used for the forecast of the terminal operations, the analysis of the workload and efficiency of the organization of the marine terminal.

  6. Mathematical model of marine diesel engine simulator for a new methodology of self propulsion tests

    Science.gov (United States)

    Izzuddin, Nur; Sunarsih, Priyanto, Agoes

    2015-05-01

    As a vessel operates in the open seas, a marine diesel engine simulator whose engine rotation is controlled to transmit through propeller shaft is a new methodology for the self propulsion tests to track the fuel saving in a real time. Considering the circumstance, this paper presents the real time of marine diesel engine simulator system to track the real performance of a ship through a computer-simulated model. A mathematical model of marine diesel engine and the propeller are used in the simulation to estimate fuel rate, engine rotating speed, thrust and torque of the propeller thus achieve the target vessel's speed. The input and output are a real time control system of fuel saving rate and propeller rotating speed representing the marine diesel engine characteristics. The self-propulsion tests in calm waters were conducted using a vessel model to validate the marine diesel engine simulator. The simulator then was used to evaluate the fuel saving by employing a new mathematical model of turbochargers for the marine diesel engine simulator. The control system developed will be beneficial for users as to analyze different condition of vessel's speed to obtain better characteristics and hence optimize the fuel saving rate.

  7. Mathematical model of marine diesel engine simulator for a new methodology of self propulsion tests

    International Nuclear Information System (INIS)

    Izzuddin, Nur; Sunarsih,; Priyanto, Agoes

    2015-01-01

    As a vessel operates in the open seas, a marine diesel engine simulator whose engine rotation is controlled to transmit through propeller shaft is a new methodology for the self propulsion tests to track the fuel saving in a real time. Considering the circumstance, this paper presents the real time of marine diesel engine simulator system to track the real performance of a ship through a computer-simulated model. A mathematical model of marine diesel engine and the propeller are used in the simulation to estimate fuel rate, engine rotating speed, thrust and torque of the propeller thus achieve the target vessel’s speed. The input and output are a real time control system of fuel saving rate and propeller rotating speed representing the marine diesel engine characteristics. The self-propulsion tests in calm waters were conducted using a vessel model to validate the marine diesel engine simulator. The simulator then was used to evaluate the fuel saving by employing a new mathematical model of turbochargers for the marine diesel engine simulator. The control system developed will be beneficial for users as to analyze different condition of vessel’s speed to obtain better characteristics and hence optimize the fuel saving rate

  8. Mathematical model of marine diesel engine simulator for a new methodology of self propulsion tests

    Energy Technology Data Exchange (ETDEWEB)

    Izzuddin, Nur; Sunarsih,; Priyanto, Agoes [Faculty of Mechanical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor (Malaysia)

    2015-05-15

    As a vessel operates in the open seas, a marine diesel engine simulator whose engine rotation is controlled to transmit through propeller shaft is a new methodology for the self propulsion tests to track the fuel saving in a real time. Considering the circumstance, this paper presents the real time of marine diesel engine simulator system to track the real performance of a ship through a computer-simulated model. A mathematical model of marine diesel engine and the propeller are used in the simulation to estimate fuel rate, engine rotating speed, thrust and torque of the propeller thus achieve the target vessel’s speed. The input and output are a real time control system of fuel saving rate and propeller rotating speed representing the marine diesel engine characteristics. The self-propulsion tests in calm waters were conducted using a vessel model to validate the marine diesel engine simulator. The simulator then was used to evaluate the fuel saving by employing a new mathematical model of turbochargers for the marine diesel engine simulator. The control system developed will be beneficial for users as to analyze different condition of vessel’s speed to obtain better characteristics and hence optimize the fuel saving rate.

  9. Levelized Cost of Energy Analysis of Marine and Hydrokinetic Reference Models: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Jenne, D. S.; Yu, Y. H.; Neary, V.

    2015-04-24

    In 2010 the U.S. Department of Energy initiated the development of six marine energy converter reference models. The reference models are point designs of well-known marine energy converters. Each device was designed to operate in a specific marine resource, instead of a generic device that can be deployed at any location. This method allows each device to be used as a benchmark for future reference model to benchmark future devices. The six designs consist of three current energy converters and three wave energy converters. The reference model project has generated both technical and economic data sets that are available in the public domain. The methodology to calculate the levelized cost of energy for the reference model project and an overall comparison of the cost of energy from these six reference-model designs are presented in this paper.

  10. Microbial and Mineral Controls on Soil Organic Carbon Decomposition: Testing the MEND Model with Data from Lab Incubations

    Science.gov (United States)

    Wang, G.; Jagadamma, S.; Steinweg, J. M.; Mayes, M. A.; Post, W. M.

    2012-12-01

    Microbes (including enzymes) and physical-chemical protection play important roles in controlling soil organic carbon (SOC) decomposition. The Microbial-ENzyme-mediated Decomposition (MEND) model was used to examine the dynamics of physically fractionated SOC pools in lab incubation experiments. The carbon pools in MEND consist of particulate, mineral-associated, dissolved organic carbon (POC, MOC, and DOC, respectively), microbial biomass, and associated exoenzymes. The following component carbon fluxes are described in MEND: POC and MOC decomposition, DOC uptake by microbes, adsorption and desorption of DOC, microbial growth and maintenance respiration, microbial mortality, and enzyme production and turnover. The kinetic parameters pertaining to these processes were determined based on the measured respiration processes and the a priori ranges/distributions of parameters. We attempted to demonstrate different dynamics of POC and MOC pools regulated by microbial-enzyme activities under different physical-chemical circumstances. Carbon pools and fluxes in the microbial-enzyme-mediated decomposition model

  11. Microbial Performance of Food Safety Control and Assurance Activities in a Fresh Produce Processing Sector Measured Using a Microbial Assessment Scheme and Statistical Modeling

    DEFF Research Database (Denmark)

    Njage, Patrick Murigu Kamau; Sawe, Chemutai Tonui; Onyango, Cecilia Moraa

    2017-01-01

    Current approaches such as inspections, audits, and end product testing cannot detect the distribution and dynamics of microbial contamination. Despite the implementation of current food safety management systems, foodborne outbreaks linked to fresh produce continue to be reported. A microbial...... assessment scheme and statistical modeling were used to systematically assess the microbial performance of core control and assurance activities in five Kenyan fresh produce processing and export companies. Generalized linear mixed models and correlated random-effects joint models for multivariate clustered...... data followed by empirical Bayes estimates enabled the analysis of the probability of contamination across critical sampling locations (CSLs) and factories as a random effect. Salmonella spp. and Listeria monocytogenes were not detected in the final products. However, none of the processors attained...

  12. A comparative study of microbial diversity and community structure in marine sediments using poly(A tailing and reverse transcription PCR

    Directory of Open Access Journals (Sweden)

    Tatsuhiko eHoshino

    2013-06-01

    Full Text Available To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA synthesis and sequencing to eliminate potential biases caused by mismatching of PCR primer sequences. The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. The sequences obtained using the ploy(A tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-polymerase chain reaction (RT-PCR with published domain-specific primers. Both methods indicated that Deltaproteobacteria are predominant in sediment (>85% of the total sequence read. The poly(A tailing method indicated that Desulfobacterales were the predominant deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. This discrepancy may have been due to low coverage of Desulfobacterales by the primers used. A comparison of library diversity indices indicated that the poly(A tailing method retrieves more phylogenetically diverse sequences from the environment. The four archaeal 16S rRNA sequences that were obtained using the poly(A tailing method formed deeply branching lineages that were related to Candidatus Parvarchaeum and the Ancient Archaeal Group. These results clearly demonstrate that poly(A tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities.

  13. Thermodynamic network model for predicting effects of substrate addition and other perturbations on subsurface microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Jack Istok; Melora Park; James McKinley; Chongxuan Liu; Lee Krumholz; Anne Spain; Aaron Peacock; Brett Baldwin

    2007-04-19

    The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on microbial growth, community composition and system geochemistry. The hypothesis is that a thermodynamic analysis of the energy-yielding growth reactions performed by defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change.

  14. Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

    Science.gov (United States)

    Ebrahimi, Ali; Or, Dani

    2015-12-01

    The constantly changing soil hydration status affects gas and nutrient diffusion through soil pores and thus the functioning of soil microbial communities. The conditions within soil aggregates are of particular interest due to limitations to oxygen diffusion into their core, and the presence of organic carbon often acting as binding agent. We developed a model for microbial life in simulated soil aggregates comprising of 3-D angular pore network model (APNM) that mimics soil hydraulic and transport properties. Within these APNM, we introduced individual motile (flagellated) microbial cells with different physiological traits that grow, disperse, and respond to local nutrients and oxygen concentrations. The model quantifies the dynamics and spatial extent of anoxic regions that vary with hydration conditions, and their role in shaping microbial community size and activity and the spatial (self) segregation of anaerobes and aerobes. Internal carbon source and opposing diffusion directions of oxygen and carbon within an aggregate were essential to emergence of stable coexistence of aerobic and anaerobic communities (anaerobes become extinct when carbon sources are external). The model illustrates a range of hydration conditions that promote or suppress denitrification or decomposition of organic matter and thus affect soil GHG emissions. Model predictions of CO2 and N2O production rates were in good agreement with limited experimental data. These limited tests support the dynamic modeling approach whereby microbial community size, composition, and spatial arrangement emerge from internal interactions within soil aggregates. The upscaling of the results to a population of aggregates of different sizes embedded in a soil profile is underway.

  15. Radiation Dose Assessment Model for Marine Biota (K-BIOTA-DYN-M)

    Energy Technology Data Exchange (ETDEWEB)

    Keum, Dong-Kwon; Kim, Byeong-Ho; Jun, In; Lim, Kwang-Muk; Choi, Yong-Ho [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-10-15

    In this study, a dynamic compartment model based on the food chain of marine biota, which can be used with easily obtainable ecological parameters, is presented to predict the activity concentration and dose rate of marine biota as a result of a nuclear. The model was applied to investigate a long-term effect of the Fukushima accident on the marine biota by using {sup 131}I, {sup 134}Cs, and {sup 137}Cs activity concentrations of seawater measured for up to about 2.5years after the accident in the port of FDNPS, which was known to be the most severely contaminated. A dynamic compartment model was presented to assess the activity concentration and whole body dose rate of marine biota, and was tested through the prediction of the activity concentration and dose rate of the marine biota using the seawater activities of {sup 131}I, {sup 134}Cs, and {sup 137}Cs measured after the accident at two locations in the port of the Fukushima Daiichi Nuclear Power Station (FDNPS), as a result the Fukushima nuclear accident that occurred on March 11, 2011. The prediction results showed the radiological effect on the population of the marine biota as a consequence of the accident was insignificant. This result is also valid for biota in a less contaminated offshore because the present assessment was made for the most highly contaminated area such as marine ecosystem in the port of FDNPS. Conclusively, the present dynamic model can be usefully applied to estimate the activity concentration and whole body dose rate of the marine biota as the consequence of a nuclear accident.

  16. Marine and Hydrokinetic Technology (MHK) Instrumentation, Measurement, and Computer Modeling Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Musial, W.; Lawson, M.; Rooney, S.

    2013-02-01

    The Marine and Hydrokinetic Technology (MHK) Instrumentation, Measurement, and Computer Modeling Workshop was hosted by the National Renewable Energy Laboratory (NREL) in Broomfield, Colorado, July 9-10, 2012. The workshop brought together over 60 experts in marine energy technologies to disseminate technical information to the marine energy community and collect information to help identify ways in which the development of a commercially viable marine energy industry can be accelerated. The workshop was comprised of plenary sessions that reviewed the state of the marine energy industry and technical sessions that covered specific topics of relevance. Each session consisted of presentations, followed by facilitated discussions. During the facilitated discussions, the session chairs posed several prepared questions to the presenters and audience to encourage communication and the exchange of ideas between technical experts. Following the workshop, attendees were asked to provide written feedback on their takeaways and their best ideas on how to accelerate the pace of marine energy technology development. The first four sections of this document give a general overview of the workshop format, provide presentation abstracts and discussion session notes, and list responses to the post-workshop questions. The final section presents key findings and conclusions from the workshop that suggest how the U.S. Department of Energy and national laboratory resources can be utilized to most effectively assist the marine energy industry.

  17. Marine and Hydrokinetic Technology (MHK) Instrumentation, Measurement, and Computer Modeling Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Musial, W. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Lawson, M. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Rooney, S. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2013-02-01

    The Marine and Hydrokinetic Technology (MHK) Instrumentation, Measurement, and Computer Modeling Workshop was hosted by the National Renewable Energy Laboratory (NREL) in Broomfield, Colorado, July 9–10, 2012. The workshop brought together over 60 experts in marine energy technologies to disseminate technical information to the marine energy community, and to collect information to help identify ways in which the development of a commercially viable marine energy industry can be accelerated. The workshop was comprised of plenary sessions that reviewed the state of the marine energy industry and technical sessions that covered specific topics of relevance. Each session consisted of presentations, followed by facilitated discussions. During the facilitated discussions, the session chairs posed several prepared questions to the presenters and audience to encourage communication and the exchange of ideas between technical experts. Following the workshop, attendees were asked to provide written feedback on their takeaways from the workshop and their best ideas on how to accelerate the pace of marine energy technology development. The first four sections of this document give a general overview of the workshop format, provide presentation abstracts, supply discussion session notes, and list responses to the post-workshop questions. The final section presents key findings and conclusions from the workshop that suggest what the most pressing MHK technology needs are and how the U.S. Department of Energy (DOE) and national laboratory resources can be utilized to assist the marine energy industry in the most effective manner.

  18. Modeling and Control of a Single-Phase Marine Cooling System

    DEFF Research Database (Denmark)

    Hansen, Michael; Stoustrup, Jakob; Bendtsen, Jan Dimon

    2013-01-01

    This paper presents two model-based control design approaches for a single-phase marine cooling system. Models are derived from first principles and aim at describing significant system dynamics including nonlinearities and transport delays, while keeping the model complexity low. The two...

  19. Microbial Degradation of Propylene Glycol - Modelling Approach of a Batch Experiment

    Science.gov (United States)

    Dathe, Annette; Fernandez, Perrine; Bakken, Lars; Bloem, Esther; French, Helen

    2016-04-01

    De-icing chemicals are applied in large amounts at airports during winter conditions to keep the runways and aircrafts ice-free. At Gardermoen airport, Norway, most of the applied chemicals can be captured, but about 10 to 20 % infiltrate into the soil along the runways and during take-off. While the commonly used propylene glycol (PG) is easily degradable by local microbial communities, its biological oxygen demand is high, anoxic zones can develop and soluble Fe+2 and Mn+2 ions eventually can reach the groundwater. The objectives of the presented study are to quantify the mechanisms, which control the order of reduction processes in an unsaturated sandy soil, and to test whether measured redox potentials can help to determine underlying biogeochemical reactions. To investigate the mechanisms of microbial degradation, the water phase of soil samples from Gardermoen Airport was replaced by deionized water with 10 mMol PG or 10 mMol glutamate and the samples were incubated at 10°C for about two weeks. The gas phase was sampled and analyzed automatically every three hours. Microbial degradation of the substrate (PG or glutamate) was modelled following a Monod kinetics using the FME (Flexible Modelling Environment) package of R (Project for Statistical Computing). The model was calibrated against measurements of O2 depletion and CO2 production. The initial concentrations of O2, CO2 and PG or glutamate are known and microbial yields and stoichiometric constants can be calculated from the measurements. Parameter values for the initial microbial population size, maximum microbial growth rate, the half saturation constant, and microbial degradation and respiration rates were fitted using the FME package. The model accounts for carbon from the substrate (PG or glutamate) incorporated into the biomass. Results are promising, but because of the large number of parameters needed to fit a Monod kinetics it is challenging to accurately model a whole redox sequence. The

  20. Some aspects of modelling microbial quality of food.

    NARCIS (Netherlands)

    Zwietering, M.H.; Rombouts, F.M.; Riet, van 't K.

    1993-01-01

    The kinetics of food deterioration reactions are important for the optimization of food chains. Different model types used to predict deterioration kinetics are briefly commented on. Objectives and needs for modelling are presented. A procedure to compare different models is given together with an

  1. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Energy Technology Data Exchange (ETDEWEB)

    He, Yujie [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Yang, Jinyan [Univ. of Georgia, Athens, GA (United States). Warnell School of Forestry and Natural Resources; Northeast Forestry Univ., Harbin (China). Center for Ecological Research; Zhuang, Qianlai [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Purdue Univ., West Lafayette, IN (United States). Dept. of Agronomy; Harden, Jennifer W. [U.S. Geological Survey, Menlo Park, CA (United States); McGuire, Anthony D. [Alaska Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, Univ. of Alaska, Fairbanks, AK (United States). U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit; Liu, Yaling [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Wang, Gangsheng [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Climate Change Science Inst. and Environmental Sciences Division; Gu, Lianhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division

    2015-11-20

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here in this study we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 PgCyr-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil RH with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  2. The UK Earth System Models Marine Biogeochemical Evaluation Toolkit, BGC-val

    Science.gov (United States)

    de Mora, Lee

    2017-04-01

    The Biogeochemical Validation toolkit, BGC-val, is a model and grid independent python-based marine model evaluation framework that automates much of the validation of the marine component of an Earth System Model. BGC-val was initially developed to be a flexible and extensible system to evaluate the spin up of the marine UK Earth System Model (UKESM). However, the grid-independence and flexibility means that it is straightforward to adapt the BGC-val framework to evaluate other marine models. In addition to the marine component of the UKESM, this toolkit has been adapted to compare multiple models, including models from the CMIP5 and iMarNet inter-comparison projects. The BGC-val toolkit produces multiple levels of analysis which are presented in a simple to use interactive html5 document. Level 1 contains time series analyses, showing the development over time of many important biogeochemical and physical ocean metrics, such as the Global primary production or the Drake passage current. The second level of BGC-val is an in-depth spatial analyses of a single point in time. This is a series of point to point comparison of model and data in various regions, such as a comparison of Surface Nitrate in the model vs data from the world ocean atlas. The third level analyses are specialised ad-hoc packages to go in-depth on a specific question, such as the development of Oxygen minimum zones in the Equatorial Pacific. In additional to the three levels, the html5 document opens with a Level 0 table showing a summary of the status of the model run. The beta version of this toolkit is available via the Plymouth Marine Laboratory Gitlab server and uses the BSD 3 clause license.

  3. Microbial and Organic Fine Particle Transport Dynamics in Streams - a Combined Experimental and Stochastic Modeling Approach

    Science.gov (United States)

    Drummond, Jen; Davies-Colley, Rob; Stott, Rebecca; Sukias, James; Nagels, John; Sharp, Alice; Packman, Aaron

    2014-05-01

    Transport dynamics of microbial cells and organic fine particles are important to stream ecology and biogeochemistry. Cells and particles continuously deposit and resuspend during downstream transport owing to a variety of processes including gravitational settling, interactions with in-stream structures or biofilms at the sediment-water interface, and hyporheic exchange and filtration within underlying sediments. Deposited cells and particles are also resuspended following increases in streamflow. Fine particle retention influences biogeochemical processing of substrates and nutrients (C, N, P), while remobilization of pathogenic microbes during flood events presents a hazard to downstream uses such as water supplies and recreation. We are conducting studies to gain insights into the dynamics of fine particles and microbes in streams, with a campaign of experiments and modeling. The results improve understanding of fine sediment transport, carbon cycling, nutrient spiraling, and microbial hazards in streams. We developed a stochastic model to describe the transport and retention of fine particles and microbes in rivers that accounts for hyporheic exchange and transport through porewaters, reversible filtration within the streambed, and microbial inactivation in the water column and subsurface. This model framework is an advance over previous work in that it incorporates detailed transport and retention processes that are amenable to measurement. Solute, particle, and microbial transport were observed both locally within sediment and at the whole-stream scale. A multi-tracer whole-stream injection experiment compared the transport and retention of a conservative solute, fluorescent fine particles, and the fecal indicator bacterium Escherichia coli. Retention occurred within both the underlying sediment bed and stands of submerged macrophytes. The results demonstrate that the combination of local measurements, whole-stream tracer experiments, and advanced modeling

  4. A dynamic mathematical model for microbial removal of pyritic sulfur from coal.

    Science.gov (United States)

    Kargi, F; Weissman, J G

    1984-06-01

    A dynamic mathematical model has been developed to describe microbial desulfurization of coal by Thiobacillus ferrooxidans. The model considers adsorption and desorption of cells on coal particles and microbial oxidation of pyritic sulfur on particle surfaces. The influence of certain parameters, such as microbial growth rate constants, adsorption-description constants, pulp density, coal particle size, initial cell and solid phase substrate concentration on the maximum rate of pyritic sulfur removal, have been elucidated. The maximum rate of pyritic sulfur removal was strongly dependent upon the number of attached cells per coal particle. At sufficiently high initial cell concentrations, the surfaces of coal particles are nearly saturated by the cells and the maximum leaching rate is limited either by total external surface area of coal particles or by the concentration of pyritic sulfur in the coal phase. The maximum volumetric rate of pyritic sulfur removal (mg S/h cm(3) mixture) increases with the pulp density of coal and reaches a saturation level at high pulp densities (e.g. 45%). The maximum rate also increases with decreasing particle diameter in a hyperbolic form. Increases in adsorption coefficient or decreases in the desorption coefficient also result in considerable improvements in this rate. The model can be applied to other systems consisting of suspended solid substrate particles in liquid medium with microbial oxidation occurring on the particle surfaces (e.g., bacterial ore leaching). The results obtained from this model are in good agreement with published experimental data on microbial desulfurization of coal and bacterial ore leaching.

  5. Model-Based Analysis of the Potential of Macroinvertebrates as Indicators for Microbial Pathogens in Rivers

    Directory of Open Access Journals (Sweden)

    Rubén Jerves-Cobo

    2018-03-01

    Full Text Available The quality of water prior to its use for drinking, farming or recreational purposes must comply with several physicochemical and microbiological standards to safeguard society and the environment. In order to satisfy these standards, expensive analyses and highly trained personnel in laboratories are required. Whereas macroinvertebrates have been used as ecological indicators to review the health of aquatic ecosystems. In this research, the relationship between microbial pathogens and macrobenthic invertebrate taxa was examined in the Machangara River located in the southern Andes of Ecuador, in which 33 sites, according to their land use, were chosen to collect physicochemical, microbiological and biological parameters. Decision tree models (DTMs were used to generate rules that link the presence and abundance of some benthic families to microbial pathogen standards. The aforementioned DTMs provide an indirect, approximate, and quick way of checking the fulfillment of Ecuadorian regulations for water use related to microbial pathogens. The models built and optimized with the WEKA package, were evaluated based on both statistical and ecological criteria to make them as clear and simple as possible. As a result, two different and reliable models were obtained, which could be used as proxy indicators in a preliminary assessment of pollution of microbial pathogens in rivers. The DTMs can be easily applied by staff with minimal training in the identification of the sensitive taxa selected by the models. The presence of selected macroinvertebrate taxa in conjunction with the decision trees can be used as a screening tool to evaluate sites that require additional follow up analyses to confirm whether microbial water quality standards are met.

  6. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    Science.gov (United States)

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

    2016-02-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  7. Responses of two nonlinear microbial models to warming and increased carbon input

    Science.gov (United States)

    Wang, Y. P.; Jiang, J.; Chen-Charpentier, B.; Agusto, F. B.; Hastings, A.; Hoffman, F.; Rasmussen, M.; Smith, M. J.; Todd-Brown, K.; Wang, Y.; Xu, X.; Luo, Y. Q.

    2016-02-01

    A number of nonlinear microbial models of soil carbon decomposition have been developed. Some of them have been applied globally but have yet to be shown to realistically represent soil carbon dynamics in the field. A thorough analysis of their key differences is needed to inform future model developments. Here we compare two nonlinear microbial models of soil carbon decomposition: one based on reverse Michaelis-Menten kinetics (model A) and the other on regular Michaelis-Menten kinetics (model B). Using analytic approximations and numerical solutions, we find that the oscillatory responses of carbon pools to a small perturbation in their initial pool sizes dampen faster in model A than in model B. Soil warming always decreases carbon storage in model A, but in model B it predominantly decreases carbon storage in cool regions and increases carbon storage in warm regions. For both models, the CO2 efflux from soil carbon decomposition reaches a maximum value some time after increased carbon input (as in priming experiments). This maximum CO2 efflux (Fmax) decreases with an increase in soil temperature in both models. However, the sensitivity of Fmax to the increased amount of carbon input increases with soil temperature in model A but decreases monotonically with an increase in soil temperature in model B. These differences in the responses to soil warming and carbon input between the two nonlinear models can be used to discern which model is more realistic when compared to results from field or laboratory experiments. These insights will contribute to an improved understanding of the significance of soil microbial processes in soil carbon responses to future climate change.

  8. Influence of excessive exercise on immunity, metabolism, and gut microbial diversity in an overtraining mice model.

    Science.gov (United States)

    Yuan, Xin; Xu, Shijie; Huang, Haiyang; Liang, Jian; Wu, Yayun; Li, Chujie; Yuan, Huiqi; Zhao, Xuejie; Lai, Xiaoping; Hou, Shaozhen

    2018-01-24

    The purpose of this study was to evaluate the negative influence of excessive exercise on immunity, substance and energy metabolism as well as gut microbiota in mice. Firstly, an overtraining model of Male Kunming mice was established by high-intensity swimming exercise for 4 weeks. Then, a series of evaluation indicators, including the routine blood analysis, immune organ coefficient, digestive enzymes, and aquaporins expression levels of small intestine and colon tissue, histological examinations of liver, spleen, small intestine, and colon, were determined based on this model. Furthermore, 16S rRNA gene sequencing was also employed to measure the microbial composition in gut. The results found that immune parameters, substance and energy metabolism of all mice was altered and disturbed after high-intensity swimming for 4 weeks, led to an atrophy of thymus and spleen as well as abnormal structural changes in liver when compared to non-swimming mice. Besides, excessive swimming mice had lower microbial diversity compared to non-swimming mice. However, there was no significant difference in gut microbial taxa between the two groups. The data indicated that excessive exercise exhibits negative impacts on immunity, substance and energy metabolism as well as gut microbial diversity. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Calibrated Blade-Element/Momentum Theory Aerodynamic Model of the MARIN Stock Wind Turbine: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Goupee, A.; Kimball, R.; de Ridder, E. J.; Helder, J.; Robertson, A.; Jonkman, J.

    2015-04-02

    In this paper, a calibrated blade-element/momentum theory aerodynamic model of the MARIN stock wind turbine is developed and documented. The model is created using open-source software and calibrated to closely emulate experimental data obtained by the DeepCwind Consortium using a genetic algorithm optimization routine. The provided model will be useful for those interested in validating interested in validating floating wind turbine numerical simulators that rely on experiments utilizing the MARIN stock wind turbine—for example, the International Energy Agency Wind Task 30’s Offshore Code Comparison Collaboration Continued, with Correlation project.

  10. Enhancing metaproteomics-The value of models and defined environmental microbial systems

    Energy Technology Data Exchange (ETDEWEB)

    Herbst, Florian-Alexander [Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg Denmark; Lünsmann, Vanessa [Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig Germany; Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig Germany; Kjeldal, Henrik [Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg Denmark; Jehmlich, Nico [Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig Germany; Tholey, Andreas [Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel Germany; von Bergen, Martin [Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg Denmark; Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig Germany; Nielsen, Jeppe Lund [Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg Denmark; Hettich, Robert L. [Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge TN USA; Seifert, Jana [Institute of Animal Science, University of Hohenheim, Stuttgart Germany; Nielsen, Per Halkjaer [Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg Denmark

    2016-01-21

    Metaproteomics - the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time - added unique features and possibilities to study environmental microbial communities and to unravel these “black boxes”. New technical challenges arose which were not an issue for classical proteome analytics before and choosing the appropriate model system applicable to the research question can be difficult. Here, we reviewed different model systems for metaproteome analysis. Following a short introduction to microbial communities and systems, we discussed the most used systems ranging from technical systems over rhizospheric models to systems for the medical field. This includes acid mine drainage, anaerobic digesters, activated sludge, planted fixed bed reactors, gastrointestinal simulators and in vivo models. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial responses and ecological distribution of member organisms. In the future, novel improvements are necessary to fully engage complex environmental systems.

  11. Complete nucleotide sequence and analysis of two conjugative broad host range plasmids from a marine microbial biofilm.

    Directory of Open Access Journals (Sweden)

    Peter Norberg

    Full Text Available The complete nucleotide sequence of plasmids pMCBF1 and pMCBF6 was determined and analyzed. pMCBF1 and pMCBF6 form a novel clade within the IncP-1 plasmid family designated IncP-1 ς. The plasmids were exogenously isolated earlier from a marine biofilm. pMCBF1 (62 689 base pairs; bp and pMCBF6 (66 729 bp have identical backbones, but differ in their mercury resistance transposons. pMCBF1 carries Tn5053 and pMCBF6 carries Tn5058. Both are flanked by 5 bp direct repeats, typical of replicative transposition. Both insertions are in the vicinity of a resolvase gene in the backbone, supporting the idea that both transposons are "res-site hunters" that preferably insert close to and use external resolvase functions. The similarity of the backbones indicates recent insertion of the two transposons and the ongoing dynamics of plasmid evolution in marine biofilms. Both plasmids also carry the insertion sequence ISPst1, albeit without flanking repeats. ISPs1is located in an unusual site within the control region of the plasmid. In contrast to most known IncP-1 plasmids the pMCBF1/pMCBF6 backbone has no insert between the replication initiation gene (trfA and the vegetative replication origin (oriV. One pMCBF1/pMCBF6 block of about 2.5 kilo bases (kb has no similarity with known sequences in the databases. Furthermore, insertion of three genes with similarity to the multidrug efflux pump operon mexEF and a gene from the NodT family of the tripartite multi-drug resistance-nodulation-division (RND system in Pseudomonas aeruginosa was found. They do not seem to confer antibiotic resistance to the hosts of pMCBF1/pMCBF6, but the presence of RND on promiscuous plasmids may have serious implications for the spread of antibiotic multi-resistance.

  12. Responses of two nonlinear microbial models to warming or increased carbon input

    Science.gov (United States)

    Wang, Y. P.; Jiang, J.; Chen-Charpentier, B.; Agusto, F. B.; Hastings, A.; Hoffman, F.; Rasmussen, M.; Smith, M. J.; Todd-Brown, K.; Wang, Y.; Xu, X.; Luo, Y. Q.

    2015-09-01

    A number of nonlinear microbial models of soil carbon decomposition have been developed. Some of them have been applied globally but have yet to be shown to realistically represent soil carbon dynamics in the field. Therefore a thorough analysis of their key differences will be very useful for the future development of these models. Here we compare two nonlinear microbial models of soil carbon decomposition: one is based on reverse Michaelis-Menten kinetics (model A) and the other on regular Michaelis-Menten kinetics (model B). Using a combination of analytic solutions and numerical simulations, we find that the oscillatory responses of carbon pools model A to a small perturbation in the initial pool sizes have a higher frequency and damps faster than model B. In response to soil warming, soil carbon always decreases in model A; but likely decreases in cool regions and increases in warm regions in model B. Maximum CO2 efflux from soil carbon decomposition (Fmax) after an increased carbon addition decreases with an increase in soil temperature in both models, and the sensitivity of Fmax to the amount of carbon input increases with soil temperature in model A; but decreases monotonically with an increase in soil temperature in model B. These differences in the responses to soil warming and carbon input between the two nonlinear models can be used to differentiate which model is more realistic with field or laboratory experiments. This will lead to a better understanding of the significance of soil microbial processes in the responses of soil carbon to future climate change at regional or global scales.

  13. Genomic insights into the marine sponge microbiome.

    Science.gov (United States)

    Hentschel, Ute; Piel, Jörn; Degnan, Sandie M; Taylor, Michael W

    2012-09-01

    Marine sponges (phylum Porifera) often contain dense and diverse microbial communities, which can constitute up to 35% of the sponge biomass. The genome of one sponge, Amphimedon queenslandica, was recently sequenced, and this has provided new insights into the origins of animal evolution. Complementary efforts to sequence the genomes of uncultivated sponge symbionts have yielded the first glimpse of how these intimate partnerships are formed. The remarkable microbial and chemical diversity of the sponge-microorganism association, coupled with its postulated antiquity, makes sponges important model systems for the study of metazoan host-microorganism interactions, and their evolution, as well as for enabling access to biotechnologically important symbiont-derived natural products. In this Review, we discuss our current understanding of the interactions between marine sponges and their microbial symbiotic consortia, and highlight recent insights into these relationships from genomic studies.

  14. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

    International Nuclear Information System (INIS)

    Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

    2011-01-01

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species, multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  15. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

    Science.gov (United States)

    Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

    2011-03-01

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  16. Marine Biogeochemistry Under The Influence of Fish And Fisheries: An Ecosystem Modeling Study

    Science.gov (United States)

    Disa, Deniz; Akoglu, Ekin; Salihoglu, Baris

    2017-04-01

    The ocean and the marine ecosystems are important controllers of the global carbon cycle. They play a pivotal role in capturing atmospheric carbon into the ocean body, transforming it into organic carbon through photosynthesis and transporting it to the depths of the ocean. Fish, which has a significant role in the marine food webs, is thought to have a considerable impact on carbon export. More specifically, fish has a control on plankton dynamics as a predator, it provides nutrient to the ecosystem by its metabolic activities and it has the ability of moving actively and transporting materials. Fishing is also expected to impact carbon cycle because it directly changes the fish biomasses. However, how fish impacts the biogeochemistry of marine ecosystems is not studied extensively. The aim of this study is to analyze the impact of fish and fisheries on marine biogeochemical processes by setting up an end-to-end model, which simulates lower and higher tropic levels of marine ecosystems simultaneously. For this purpose, a one dimensional biogeochemical model simulating lower tropic level dynamics (e.g. carbon export, nutrient cycles) and an food web model simulating fisheries exploitation and higher tropic level dynamics were online and two-way coupled. Representing the marine ecosystem from one end to the other, the coupled model served as a tool for the analysis of fishing impacts on marine biogeochemical dynamics. Results obtained after incorporation of higher trophic level model changed the plankton compositions and enhanced detritus pools and increased carbon export. Additionally, our model showed that active movement of fish contributed to transport of carbon from surface to the deeper parts of the ocean. Moreover, results after applying different fishing intensities indicated that changes in fisheries exploitation levels directly influence the marine nutrient cycles and hence, the carbon export. Depending on the target and the intensity of fisheries

  17. Effect of different enrichment strategies on microbial community structure in petroleum-contaminated marine sediment in Dalian, China.

    Science.gov (United States)

    Chen, Chao; Liu, Qiu; Liu, Changjian; Yu, Jicheng

    2017-04-15

    An oil spill occurred at Xingang Port, Dalian, China in 2010. Four years after this spill, oil contamination was still detected in samples collected nearby. In this study, the strains that evolved in the sediment were screened by high-throughput sequencing technology. Most of these strains were genera reported to have functions associated with crude oil biodegradation. The diversities and numbers of microbes were monitored through enrichment culturing; the dominant strains propagated at first, but the enrichment could not be continued, which indicated that the prolonged culture was not effective in the enrichment of the micro-consortium. Oxygen was also observed to affect the propagation of the dominant microbes. The results showed the role of culture strategies and oxygen in the enrichment of the petroleum-degrading microbes. Therefore, dominant strains could be screened by optimizing both the enrichment time and oxygen concentration used for culturing to facilitate oil biodegradation in the marine ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Modeling of vortex dynamics in the wake of a marine propeller

    NARCIS (Netherlands)

    Muscari, R.; Di Mascio, A.; Verzicco, Roberto

    2013-01-01

    The flow past a rotating marine propeller is analyzed with the aim of establishing limits and capabilities and, hence, the field of applicability of different turbulence modeling approaches for this class of problems. To this purpose the eddy viscosity model of Spalart and Allmaras (1994) [1] and

  19. Scour around a perforated disk modeling a marine hydrokinetic device

    Science.gov (United States)

    Beninati, M. L.; Soliani, G.; Zhou, C. C.; Krane, M.; Fontaine, A.

    2013-12-01

    A study was conducted to investigate the behavior of scour hole dimensions and scour rates around a bottom-mounted cylindrical support structure of a perforated disk. The experiments focus on collecting temporal variations of scour depth around the support structure of the perforated disk for two scour regimes: transitional (ReD = 8500 and 9400) and live-bed (ReD = 10200). A perforated disk is used to approximate the drag of a submerged, horizontal axis, marine hydrokinetic (MHK) turbine. The goal is to compare the scour behavior around a perforated disk to that of a marine hydrokinetic (MHK) device. This study is motivated by the need to predict the environmental effect of MHK devices on an erodible bed. Testing is conducted in the small-scale hydraulic flume facility (1.2 m wide, 0.38 m deep, and 9.75 m long) at Bucknell University. The base of the support structure is marked incrementally to allow for time based observations of changes in scour depth. Bed form topologies are then acquired after a three hour time interval using a 2D sediment bed profiler. Experimental results show that scour rate is dependent on flow speed. Additionally, an increase in scour hole size occurs as the scour conditions are varied from transitional to live-bed.

  20. Microbial and genomic characterization of Geobacillus thermodenitrificans OS27, a marine thermophile that degrades diverse raw seaweeds.

    Science.gov (United States)

    Fujii, Kenta; Tominaga, Yurie; Okunaka, Jyumpei; Yagi, Hisashi; Ohshiro, Takashi; Suzuki, Hirokazu

    2018-04-04

    Seaweeds are a nonlignocellulosic biomass, but they are often abundant in unique polysaccharides that common microbes can hardly utilize; therefore, polysaccharide degradation is key for the full utilization of seaweed biomass. Here, we isolated 13 thermophiles from seaweed homogenates that had been incubated at high temperature. All of the isolates were Gram-positive and preferentially grew at 60-70 °C. Most formed endospores and were tolerant to seawater salinity. Despite different sources, all isolates were identical regarding 16S rRNA gene sequences and were categorized as Geobacillus thermodenitrificans. Their growth occurred on seaweed polysaccharides with different profiles but required amino acids and/or vitamins, implying that they existed as proliferative cells by utilizing nutrients on seaweed viscous surfaces. Among 13 isolates, strain OS27 was further characterized to show that it can utilize a diverse range of seaweed polysaccharides and hemicelluloses. Notably, strain OS27 degraded raw seaweeds while releasing soluble saccharides. The degradation seemed to depend on enzymes that were extracellularly produced in an inducible manner. The strain could be genetically modified to produce heterologous endoglucanase, providing a transformant that degrades more diverse seaweeds with higher efficiency. The draft sequences of the OS27 genome contained 3766 coding sequences, which included intact genes for 28 glycoside hydrolases and many hypothetical proteins unusual among G. thermodenitrificans. These results suggest that G. thermodenitrificans OS27 serves as a genetic resource for thermostable enzymes to degrade seaweeds and potentially as a microbial platform for high temperature seaweed biorefinery via genetic modification.

  1. Modeling the mutualistic interactions between tubeworms and microbial consortia.

    Directory of Open Access Journals (Sweden)

    Erik E Cordes

    2005-03-01

    Full Text Available The deep-sea vestimentiferan tubeworm Lamellibrachia luymesi forms large aggregations at hydrocarbon seeps in the Gulf of Mexico that may persist for over 250 y. Here, we present the results of a diagenetic model in which tubeworm aggregation persistence is achieved through augmentation of the supply of sulfate to hydrocarbon seep sediments. In the model, L. luymesi releases the sulfate generated by its internal, chemoautotrophic, sulfide-oxidizing symbionts through posterior root-like extensions of its body. The sulfate fuels sulfate reduction, commonly coupled to anaerobic methane oxidation and hydrocarbon degradation by bacterial-archaeal consortia. If sulfate is released by the tubeworms, sulfide generation mainly by hydrocarbon degradation is sufficient to support moderate-sized aggregations of L. luymesi for hundreds of years. The results of this model expand our concept of the potential benefits derived from complex interspecific relationships, in this case involving members of all three domains of life.

  2. Final Report Coupling in silico microbial models with reactive transport models to predict the fate of contaminants in the subsurface.

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R.

    2012-10-31

    This project successfully accomplished its goal of coupling genome-scale metabolic models with hydrological and geochemical models to predict the activity of subsurface microorganisms during uranium bioremediation. Furthermore, it was demonstrated how this modeling approach can be used to develop new strategies to optimize bioremediation. The approach of coupling genome-scale metabolic models with reactive transport modeling is now well enough established that it has been adopted by other DOE investigators studying uranium bioremediation. Furthermore, the basic principles developed during our studies will be applicable to much broader investigations of microbial activities, not only for other types of bioremediation, but microbial metabolism in diversity of environments. This approach has the potential to make an important contribution to predicting the impact of environmental perturbations on the cycling of carbon and other biogeochemical cycles.

  3. Microbial comparative pan-genomics using binomial mixture models

    DEFF Research Database (Denmark)

    Ussery, David; Snipen, L; Almøy, T

    2009-01-01

    The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter...... occurring genes in the population. CONCLUSION: Analyzing pan-genomics data with binomial mixture models is a way to handle dependencies between genomes, which we find is always present. A bottleneck in the estimation procedure is the annotation of rarely occurring genes....

  4. Different Mechanisms of Soil Microbial Response to Global Change Result in Different Outcomes in the MIMICS-CN Model

    Science.gov (United States)

    Kyker-Snowman, E.; Wieder, W. R.; Grandy, S.

    2017-12-01

    Microbial-explicit models of soil carbon (C) and nitrogen (N) cycling have improved upon simulations of C and N stocks and flows at site-to-global scales relative to traditional first-order linear models. However, the response of microbial-explicit soil models to global change factors depends upon which parameters and processes in a model are altered by those factors. We used the MIcrobial-MIneral Carbon Stabilization Model with coupled N cycling (MIMICS-CN) to compare modeled responses to changes in temperature and plant inputs at two previously-modeled sites (Harvard Forest and Kellogg Biological Station). We spun the model up to equilibrium, applied each perturbation, and evaluated 15 years of post-perturbation C and N pools and fluxes. To model the effect of increasing temperatures, we independently examined the impact of decreasing microbial C use efficiency (CUE), increasing the rate of microbial turnover, and increasing Michaelis-Menten kinetic rates of litter decomposition, plus several combinations of the three. For plant inputs, we ran simulations with stepwise increases in metabolic litter, structural litter, whole litter (structural and metabolic), or labile soil C. The cumulative change in soil C or N varied in both sign and magnitude across simulations. For example, increasing kinetic rates of litter decomposition resulted in net releases of both C and N from soil pools, while decreasing CUE produced short-term increases in respiration but long-term accumulation of C in litter pools and shifts in soil C:N as microbial demand for C increased and biomass declined. Given that soil N cycling constrains the response of plant productivity to global change and that soils generate a large amount of uncertainty in current earth system models, microbial-explicit models are a critical opportunity to advance the modeled representation of soils. However, microbial-explicit models must be improved by experiments to isolate the physiological and stoichiometric

  5. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement.

    Science.gov (United States)

    Xu, Chuan; Liu, Lili; Zhang, Zhao; Jin, Danfeng; Qiu, Juanping; Chen, Ming

    2013-01-01

    In the past few decades, despite all the significant achievements in industrial microbial improvement, the approaches of traditional random mutation and selection as well as the rational metabolic engineering based on the local knowledge cannot meet today's needs. With rapid reconstructions and accurate in silico simulations, genome-scale metabolic model (GSMM) has become an indispensable tool to study the microbial metabolism and design strain improvements. In this review, we highlight the application of GSMM in guiding microbial improvements focusing on a systematic strategy and its achievements in different industrial fields. This strategy includes a repetitive process with four steps: essential data acquisition, GSMM reconstruction, constraints-based optimizing simulation, and experimental validation, in which the second and third steps are the centerpiece. The achievements presented here belong to different industrial application fields, including food and nutrients, biopharmaceuticals, biopolymers, microbial biofuel, and bioremediation. This strategy and its achievements demonstrate a momentous guidance of GSMM for metabolic engineering breeding of industrial microbes. More efforts are required to extend this kind of study in the meantime.

  6. Methymercury Formation in Marine and Freshwater Systems: Sediment Characteristics, Microbial Activity and SRB Phylogeny Control Formation Rates and Food-Chain Exposure

    Science.gov (United States)

    King, J. K.; Saunders, F. M.

    2004-05-01

    Mercury research in freshwater and marine systems suggests that sediment characteristics such as organic substrate, mercury speciation, and sulfate/sulfide concentrations influence availability of inorganic mercury for methylation. Similarly, sediment characteristics also influence sulfate-reducing bacterial (SRB) respiration as well as the presence/distribution of phylogenetic groups responsible for mercury methylation. Our work illustrates that the process of methylmercury formation in freshwater and marine systems are not dissimilar. Rather, the same geochemical parameters and SRB phylogenetic groups determine the propensity for methylmercury formation and are applicable in both fresh- and marine-water systems. The presentation will include our integration of sediment geochemical and microbial parameters affecting mercury methylation in specific freshwater and marine systems. Constructed wetlands planted with Schoenoplectus californicus and amended with gypsum (CaSO4) have demonstrated a capacity to remove inorganic mercury from industrial outfalls. However, bioaccumulation studies of periphyton, eastern mosquitofish (Gambusia holbrooki) and lake chubsucker (Erimyzon sucetta) were conducted in order to ascertain the availability of wetland-generated methylmercury to biota. Total mercury concentrations in mosquitofish from non-sulfate treated controls and the reference location were significantly lower than those from the low and high sulfate treatments while mean total mercury concentrations in lake chubsuckers were also significantly elevated in the high sulfate treatment compared to the low sulfate, control and reference populations. Methylmercury concentrations in periphyton also corresponded with mercury levels found in the tissue of the lake chubsuckers, and these findings fit well given the trophic levels identified for both species of fish. Overall, data from this study suggest that the initial use of gypsum to accelerate the maturity of a constructed

  7. A Modeling Comparison of Methanogenesis from Noncompetitive vs Competitive Substrates in a Simulated Hypersaline Microbial Mat

    Science.gov (United States)

    Decker, K. L.; Potter, C.; Hoehler, T.

    2005-12-01

    The well-documented assumption about methanogens that co-occur in hypersaline mat communities with sulfate-reducing bacteria (SRB) is that they rely entirely on non-competitive substrates for methanogenesis. The reason for this is that during sulfate reduction, sulfur-reducing bacteria efficiently utilize H2, leaving a concentration too low for methanogenesis. Early results from recent work on a hypersaline microbial mat from salt evaporation ponds of Guerrero Negro, Baja, Mexico cast doubt that methanogenesis only occurs via non-competitive substrates, because it shows an excess of H2 in the mat rather than a paucity. We explore the use of our simulation model of the microbial biogeochemistry of a hypersaline mat (named MBGC) to compare methane production rates in a 1 cm thick mat when the methanogens use competitive substrates versus noncompetitive substrates. In the `non-competitive substrate' version of the model, methanogens rely exclusively on methylated amines that are accumulated as compatible solutes in cyanobacteria and released after lysis. In contrast, the `competitive substrate' models examine methanogen use of substrates (such as H2 + acetate) with different SRB population sizes (from absent to low). The comparison of these models of methane and sulfide biogeochemistry of a hypersaline mat has both ecological and geobiological significance, as one hypothesis of Archean microbial mats is that they existed in a low sulfate environment.

  8. Final Report of the Mid-Atlantic Marine Wildlife Surveys, Modeling, and Data

    Energy Technology Data Exchange (ETDEWEB)

    Saracino-Brown, Jocelyn [Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States); Smith, Courtney [Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States); Gilman, Patrick [Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)

    2013-07-01

    The Wind Program hosted a two-day workshop on July 24-25, 2012 with scientists and regulators engaged in marine ecological survey, modeling, and database efforts pertaining to the waters of the Mid-Atlantic region. The workshop was planned by Federal agency, academic, and private partners to promote collaboration between ongoing offshore ecological survey efforts, and to promote the collaborative development of complementary predictive models and compatible databases. The meeting primarily focused on efforts to establish and predict marine mammal, seabird, and sea turtle abundance, density, and distributions extending from the shoreline to the edge of the Exclusive Economic Zone between Nantucket Sound, Massachusetts and Cape Hatteras, North Carolina.

  9. Conservation physiology of marine fishes: advancing the predictive capacity of models.

    Science.gov (United States)

    Jørgensen, Christian; Peck, Myron A; Antognarelli, Fabio; Azzurro, Ernesto; Burrows, Michael T; Cheung, William W L; Cucco, Andrea; Holt, Rebecca E; Huebert, Klaus B; Marras, Stefano; McKenzie, David; Metcalfe, Julian; Perez-Ruzafa, Angel; Sinerchia, Matteo; Fleng Steffensen, John; Teal, Lorna R; Domenici, Paolo

    2012-12-23

    At the end of May, 17 scientists involved in an EU COST Action on Conservation Physiology of Marine Fishes met in Oristano, Sardinia, to discuss how physiology can be better used in modelling tools to aid in management of marine ecosystems. Current modelling approaches incorporate physiology to different extents, ranging from no explicit consideration to detailed physiological mechanisms, and across scales from a single fish to global fishery resources. Biologists from different sub-disciplines are collaborating to rise to the challenge of projecting future changes in distribution and productivity, assessing risks for local populations, or predicting and mitigating the spread of invasive species.

  10. Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors.

    Directory of Open Access Journals (Sweden)

    Igor Shuryak

    Full Text Available Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1 bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA; (2 fungi isolated from the Chernobyl nuclear-power plant (Ukraine buildings after the accident; (3 yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s among biologically-plausible alternatives. Our analysis suggests the following: (1 Both radionuclides and co-occurring chemical contaminants (e.g. NO2 are important for explaining microbial responses to radioactive contamination. (2 Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3 The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4 Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1 the most severe effects (e.g. extinction on microbial populations may occur when unfavorable environmental

  11. Bifurcations of a periodically forced microbial continuous culture model with restrained growth rate

    Science.gov (United States)

    Ren, Jingli; Yuan, Qigang

    2017-08-01

    A three dimensional microbial continuous culture model with a restrained microbial growth rate is studied in this paper. Two types of dilution rates are considered to investigate the dynamic behaviors of the model. For the unforced system, fold bifurcation and Hopf bifurcation are detected, and numerical simulations reveal that the system undergoes degenerate Hopf bifurcation. When the system is periodically forced, bifurcation diagrams for periodic solutions of period-one and period-two are given by researching the Poincaré map, corresponding to different bifurcation cases in the unforced system. Stable and unstable quasiperiodic solutions are obtained by Neimark-Sacker bifurcation with different parameter values. Periodic solutions of various periods can occur or disappear and even change their stability, when the Poincaré map of the forced system undergoes Neimark-Sacker bifurcation, flip bifurcation, and fold bifurcation. Chaotic attractors generated by a cascade of period doublings and some phase portraits are given at last.

  12. Mathematical modelling and analysis for a three-tiered microbial food web in a chemostat

    Directory of Open Access Journals (Sweden)

    Miled El hajji

    2017-10-01

    Full Text Available In this article, we present a mathematical six-dimensional dynamical system involving a three-tiered microbial food web without maintenance. We give a qualitative analysis of the model, and an analysis of the local stability of equilibrium points. Under general assumptions of monotonicity, we prove the uniqueness and the local stability of the positive equilibrium point corresponding to the persistence of the three bacteria. Possibilities of periodic orbits are not excluded and asymptotic coexistence is satisfied.

  13. Microbial comparative pan-genomics using binomial mixture models

    Directory of Open Access Journals (Sweden)

    Ussery David W

    2009-08-01

    Full Text Available Abstract Background The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology. Results We estimate core- and pan-genome sizes for 16 different bacterial species. The results reveal a complex dependency structure for most species, manifested as heterogeneous detection probabilities. Estimated pan-genome sizes range from small (around 2600 gene families in Buchnera aphidicola to large (around 43000 gene families in Escherichia coli. Results for Echerichia coli show that as more data become available, a larger diversity is estimated, indicating an extensive pool of rarely occurring genes in the population. Conclusion Analyzing pan-genomics data with binomial mixture models is a way to handle dependencies between genomes, which we find is always present. A bottleneck in the estimation procedure is the annotation of rarely occurring genes.

  14. The Development of Marine Accidents Human Reliability Assessment Approach: HEART Methodology and MOP Model

    Directory of Open Access Journals (Sweden)

    Ludfi Pratiwi Bowo

    2017-06-01

    Full Text Available Humans are one of the important factors in the assessment of accidents, particularly marine accidents. Hence, studies are conducted to assess the contribution of human factors in accidents. There are two generations of Human Reliability Assessment (HRA that have been developed. Those methodologies are classified by the differences of viewpoints of problem-solving, as the first generation and second generation. The accident analysis can be determined using three techniques of analysis; sequential techniques, epidemiological techniques and systemic techniques, where the marine accidents are included in the epidemiological technique. This study compares the Human Error Assessment and Reduction Technique (HEART methodology and the 4M Overturned Pyramid (MOP model, which are applied to assess marine accidents. Furthermore, the MOP model can effectively describe the relationships of other factors which affect the accidents; whereas, the HEART methodology is only focused on human factors.

  15. Marine Search and Rescue of UAV in Long-Distance Security Modeling Simulation

    Directory of Open Access Journals (Sweden)

    Zheng Lei

    2017-11-01

    Full Text Available Long-distance safety of Marine search and rescue using drones can improve the searching speed. The current method is based on the long distance security classification of UAV.The degree of accuracy is low. A long-distance security modeling approach based on ArduinoMiniPro’s Marine search-and-rescue applying UAV is proposed. The method puts the fault tree analysis and relevant calculation for risk identification into use. The main factors affecting the safety of unmanned aerial vehicle (UAV are long-distance searching and rescuing. The experimental results show that the proposed method can effectively build modeling for the long-distance safety of the Marine search and rescue UAV

  16. A mechanistic model of microbial competition in the rhizosphere of wetland plants

    Science.gov (United States)

    Aslkhodapasand, F.; Mayer, K. U.; Neumann, R. B.

    2014-12-01

    Wetlands are the largest natural source of methane to the atmosphere. Although they cover only 4-6% of earth's surface, wetlands contribute 20-39% of global methane emissions. Hollow aerenchyma tissues inside the roots, stems and leaves of plants represent one of the most important methane emission pathways for wetlands. Up to 90% of the emitted methane can diffuse through these hollow tissues that directly connect the atmosphere to the anoxic soils where methane is generated. Thus, concentrations of methane surrounding plant roots directly impact the amount of methane emitted by wetlands. Methane concentrations are controlled by a variety of microbial processes occurring in the soil around the roots of plants (aka the rhizosphere). The rhizosphere is a microbial hotspot sustained by plant inputs of organic carbon and oxygen; plant roots exude excess organic carbon generated in photosynthesis into the rhizosphere and atmospheric oxygen diffuses down to the rhizosphere through the hollow aerenchyma tissues. This environment supports a variety of microbial communities that compete with each other for available carbon and oxygen, including methanogens, methanotrophs, and heterotrophs. Methanogens ferment organic carbon into methane, a reaction that is inhibited by oxygen; methanotrophs use oxygen to oxidize methane into carbon dioxide; and heterotrophs use oxygen to oxidize organic carbon into carbon dioxide. We are interested in understanding how competition between these communities alters methane concentrations and responds to variations in plant inputs. To this end, we have developed a mechanistic root-scale model that describes microbial competition for organic carbon and oxygen in the rhizosphere of wetland plants. Our results focus on variations in rates of methane production, methane oxidation, heterotrophic respiration, and diffusion of methane into plant roots as a result of changes in carbon and oxygen inputs. The study provides insight into how plant

  17. The Impact of Consumer Phase Models in Microbial Risk Analysis

    DEFF Research Database (Denmark)

    Nauta, Maarten; Christensen, Bjarke Bak

    2011-01-01

    In quantitative microbiological risk assessment (QMRA), the consumer phase model (CPM) describes the part of the food chain between purchase of the food product at retail and exposure. Construction of a CPM is complicated by the large variation in consumer food handling practices and a limited...... availability of data. Therefore, several subjective (simplifying) assumptions have to be made when a CPM is constructed, but with a single CPM their impact on the QMRA results is unclear. We therefore compared the performance of eight published CPMs for Campylobacter in broiler meat in an example of a QMRA......, where all the CPMs were analyzed using one single input distribution of concentrations at retail, and the same dose-response relationship. It was found that, between CPMs, there may be a considerable difference in the estimated probability of illness per serving. However, the estimated relative risk...

  18. Modeling the microbial growth of two Escherichia coli strains in a multi-substrate environment

    Directory of Open Access Journals (Sweden)

    M. E. Poccia

    2014-06-01

    Full Text Available The microbial growth in multi-substrate environments may be viewed as an optimal resources allocation problem. The optimization aims at maximizing some biological objective like the biomass growth. The models developed using this hypothesis are called "cybernetic" and they represent the complex cell structure as an optimizing function that regulates the intracellular enzymatic machinery. In this work, a cybernetic model was developed to represent the growth of two E. coli strains (JM 109 and BL 21 -DE3- on a medium containing glucose and glycerol as carbon and energy sources. The model was able to accurately simulate the biomass growth, the substrates consumption and the growth-rate profiles.

  19. Marine genomics: News and views.

    Science.gov (United States)

    Ribeiro, Ângela M; Foote, Andrew D; Kupczok, Anne; Frazão, Bárbara; Limborg, Morten T; Piñeiro, Rosalía; Abalde, Samuel; Rocha, Sara; da Fonseca, Rute R

    2017-02-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag between observed and estimated diversity is in part due to the elusiveness of most aquatic species and the technical difficulties of exploring extreme environments, as for instance the abyssal plains and polar waters. In the last decade, the rapid development of affordable and flexible high-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Dynamic relationships between microbial biomass, respiration, inorganic nutrients and enzyme activities: informing enzyme based decomposition models

    Directory of Open Access Journals (Sweden)

    Daryl L Moorhead

    2013-08-01

    Full Text Available We re-examined data from a recent litter decay study to determine if additional insights could be gained to inform decomposition modeling. Rinkes et al. (2013 conducted 14-day laboratory incubations of sugar maple (Acer saccharum or white oak (Quercus alba leaves, mixed with sand (0.4% organic C content or loam (4.1% organic C. They measured microbial biomass C, carbon dioxide efflux, soil ammonium, nitrate, and phosphate concentrations, and β-glucosidase (BG, β-N-acetyl-glucosaminidase (NAG, and acid phosphatase (AP activities on days 1, 3, and 14. Analyses of relationships among variables yielded different insights than original analyses of individual variables. For example, although respiration rates per g soil were higher for loam than sand, rates per g soil C were actually higher for sand than loam, and rates per g microbial C showed little difference between treatments. Microbial biomass C peaked on day 3 when biomass-specific activities of enzymes were lowest, suggesting uptake of litter C without extracellular hydrolysis. This result refuted a common model assumption that all enzyme production is constitutive and thus proportional to biomass, and/or indicated that part of litter decay is independent of enzyme activity. The length and angle of vectors defined by ratios of enzyme activities (BG/NAG versus BG/AP represent relative microbial investments in C (length, and N and P (angle acquiring enzymes. Shorter lengths on day 3 suggested low C limitation, whereas greater lengths on day 14 suggested an increase in C limitation with decay. The soils and litter in this study generally had stronger P limitation (angles > 45˚. Reductions in vector angles to < 45˚ for sand by day 14 suggested a shift to N limitation. These relational variables inform enzyme-based models, and are usually much less ambiguous when obtained from a single study in which measurements were made on the same samples than when extrapolated from separate studies.

  1. A QSAR approach for virtual screening of lead-like molecules en route to antitumor and antibiotic drugs from marine and microbial natural products

    Directory of Open Access Journals (Sweden)

    Florbela Pereira

    2014-05-01

    Figure 1. The unreported 15 lead antibiotic MNPs and MbNPs from AntiMarin database, using the best Rfs antibiotic model with a probability of being antibiotic greater than or equal to 0.8. Figure 2. The selected 4 lead antitumor MNPs and MbNPs from the AntiMarin database, using the best Rfs antitumor model with a probability of being antitumor greater than or equal to 0.8. The present work corroborates by one side the results of our previous work6 and enables the presentation of a new set of possible lead like bioactive compounds. Additionally, it is shown the usefulness of quantum-chemical descriptors in the discrimination of biological active and inactive compounds. The use of the εHOMO quantum-chemical descriptor in the discrimination of large scale data sets of lead-like or drug-like compounds has never been reported. This approach results in the reduction, in great extent, of the number of compounds used in real screens, and it reinforces the results of our previous work. Furthermore, besides the virtual screening, the computational methods can be very useful to build appropriate databases, allowing for effective shortcuts of NP extracts dereplication procedures, which will certainly result in increasing the efficiency of drug discovery.

  2. A Comparison of Modeling Approaches in Simulating Chlorinated Ethene Removal in a Constructed Wetland by a Microbial Consortia

    National Research Council Canada - National Science Library

    Campbell, Jason

    2002-01-01

    ... of the modeling approaches affect simulation results. Concepts like microbial growth in the form of a biofilm and spatially varying contaminant concentrations bring the validity of the CSTR assumption into question...

  3. Quantitative Microbial Risk Assessment Tutorial Installation of Software for Watershed Modeling in Support of QMRA - Updated 2017

    Science.gov (United States)

    This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling: • QMRA Installation • SDMProjectBuilder (which includes the Mi...

  4. A Comparison of Modeling Approaches in Simulating Chlorinated Ethene Removal in a Constructed Wetland by a Microbial Consortia

    National Research Council Canada - National Science Library

    Campbell, Jason

    2002-01-01

    The purpose of this study is to compare different approaches to modeling the reductive dechlorination of chlorinated ethenes in the anaerobic region of an upward flow constructed wetland by microbial consortia...

  5. Dynamics of development and dispersal in sessile microbial communities: examples from Pseudomonas aeruginosa and Pseudomonas putida model biofilms

    DEFF Research Database (Denmark)

    Klausen, M.; Gjermansen, Morten; Kreft, J.-U.

    2006-01-01

    Surface-associated microbial communities in many cases display dynamic developmental patterns. Model biofilms formed by Pseudomonas aeruginosa and Pseudomonas putida in laboratory flow-chamber setups represent examples of such behaviour. Dependent on the experimental conditions the bacteria...

  6. Using numerical model simulations to improve the understanding of micro-plastic distribution and pathways in the marine environment

    NARCIS (Netherlands)

    Hardesty, Britta D.; Harari, Joseph; Isobe, Atsuhiko; Lebreton, Laurent; Maximenko, Nikolai; Potemra, Jim; van Sebille, Erik; Vethaak, A.Dick; Wilcox, Chris

    2017-01-01

    Numerical modeling is one of the key tools with which we can gain insight into the distribution of marine litter, especially micro-plastics. Over the past decade, a series of numerical simulations have been constructed that specifically target floating marine litter, based on ocean models of various

  7. Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

    NARCIS (Netherlands)

    M.J.A. van Hoek (Milan); R.M.H. Merks (Roeland)

    2017-01-01

    textabstractBackground: The human gut contains approximately 1014 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides,

  8. Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

    NARCIS (Netherlands)

    Hoek, van M.J.A.; Merks, R.M.H.

    2017-01-01

    BACKGROUND:The human gut contains approximately 10(14) bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short

  9. Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

    NARCIS (Netherlands)

    M.J.A. van Hoek (Milan); R.M.H. Merks (Roeland)

    2016-01-01

    textabstractBackground: The human gut contains approximately 10e+14 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down food sources that our own digestive enzymes cannot handle, including complex polysaccharides,

  10. Global distribution and climate forcing of marine organic aerosol: 1. Model improvements and evaluation

    Directory of Open Access Journals (Sweden)

    N. Meskhidze

    2011-11-01

    Full Text Available Marine organic aerosol emissions have been implemented and evaluated within the National Center of Atmospheric Research (NCAR's Community Atmosphere Model (CAM5 with the Pacific Northwest National Laboratory's 7-mode Modal Aerosol Module (MAM-7. Emissions of marine primary organic aerosols (POA, phytoplankton-produced isoprene- and monoterpenes-derived secondary organic aerosols (SOA and methane sulfonate (MS are shown to affect surface concentrations of organic aerosols in remote marine regions. Global emissions of submicron marine POA is estimated to be 7.9 and 9.4 Tg yr−1, for the Gantt et al. (2011 and Vignati et al. (2010 emission parameterizations, respectively. Marine sources of SOA and particulate MS (containing both sulfur and carbon atoms contribute an additional 0.2 and 5.1 Tg yr−1, respectively. Widespread areas over productive waters of the Northern Atlantic, Northern Pacific, and the Southern Ocean show marine-source submicron organic aerosol surface concentrations of 100 ng m−3, with values up to 400 ng m−3 over biologically productive areas. Comparison of long-term surface observations of water insoluble organic matter (WIOM with POA concentrations from the two emission parameterizations shows that despite revealed discrepancies (often more than a factor of 2, both Gantt et al. (2011 and Vignati et al. (2010 formulations are able to capture the magnitude of marine organic aerosol concentrations, with the Gantt et al. (2011 parameterization attaining better seasonality. Model simulations show that the mixing state of the marine POA can impact the surface number concentration of cloud condensation nuclei (CCN. The largest increases (up to 20% in CCN (at a supersaturation (S of 0.2% number concentration are obtained over biologically productive ocean waters when marine organic aerosol is assumed to be externally mixed with sea-salt. Assuming

  11. A stepwise-cluster microbial biomass inference model in food waste composting

    International Nuclear Information System (INIS)

    Sun Wei; Huang, Guo H.; Zeng Guangming; Qin Xiaosheng; Sun Xueling

    2009-01-01

    A stepwise-cluster microbial biomass inference (SMI) model was developed through introducing stepwise-cluster analysis (SCA) into composting process modeling to tackle the nonlinear relationships among state variables and microbial activities. The essence of SCA is to form a classification tree based on a series of cutting or mergence processes according to given statistical criteria. Eight runs of designed experiments in bench-scale reactors in a laboratory were constructed to demonstrate the feasibility of the proposed method. The results indicated that SMI could help establish a statistical relationship between state variables and composting microbial characteristics, where discrete and nonlinear complexities exist. Significance levels of cutting/merging were provided such that the accuracies of the developed forecasting trees were controllable. Through an attempted definition of input effects on the output in SMI, the effects of the state variables on thermophilic bacteria were ranged in a descending order as: Time (day) > moisture content (%) > ash content (%, dry) > Lower Temperature (deg. C) > pH > NH 4 + -N (mg/Kg, dry) > Total N (%, dry) > Total C (%, dry); the effects on mesophilic bacteria were ordered as: Time > Upper Temperature (deg. C) > Total N > moisture content > NH 4 + -N > Total C > pH. This study made the first attempt in applying SCA to mapping the nonlinear and discrete relationships in composting processes.

  12. Quantitative analysis of anaerobic oxidation of methane (AOM) in marine sediments: a modeling perspective

    NARCIS (Netherlands)

    Regnier, P.; Dale, A.W.; Arndt, S.; LaRowe, D.E.; Mogollon, J.M.; Van Cappellen, P.

    2011-01-01

    Recent developments in the quantitativemodeling of methane dynamics and anaerobic oxidation of methane (AOM) in marine sediments are critically reviewed. The first part of the review begins with a comparison of alternative kinetic models for AOM. The roles of bioenergetic limitations, intermediate

  13. Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild.

    Science.gov (United States)

    Hallin, Sara; Welsh, Allana; Stenström, John; Hallet, Stephanie; Enwall, Karin; Bru, David; Philippot, Laurent

    2012-01-01

    Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions. Here, we compare the functional operating range, a new concept defined as the complete range of environmental conditions under which soil microbial communities are able to maintain their functions, between four naturally assembled soil communities from a long-term fertilization experiment. A functional trait approach was adopted with denitrifiers involved in nitrogen cycling as our model soil community. Using short-term temperature and salt gradients, we show that the functional operating range was broader and process rates were higher when the soil community was phylogenetically more diverse. However, key bacterial genotypes played an important role for maintaining denitrification as an ecosystem functioning under certain conditions.

  14. Integrating "Omics" Data Into A Biogeochemical Model: A New Model Scheme To Predict Climate Feedbacks From Microbial Function In Tropical Ecosystems

    Science.gov (United States)

    Song, Y.; Yao, Q.; Wang, G.; Yang, X.; Pan, C.; Johnston, E.; Kim, M.; Konstantinidis, K.; Hazen, T.; Mayes, M. A.

    2016-12-01

    Soil microorganisms and their activities, which play a significant role in regulating carbon (C) and nutrient biogeochemical cycles, are highly responsive to changes in climate. The diversity of microorganisms, however, complicates the explicit representation of microbial and enzymatic processes in biogeochemical or earth system models. Uncertainties in accounting for microbial diversity therefore limits our ability to incorporate microbial functions into models. However, `omics technology provides abundant information to identify the structure and function of the microbial community and strengthens our ability to understand microbially-mediated C and nutrient cycles and their climate feedbacks. We collected soils from control and phosphorus (P) fertilized plots at the Gigante Peninsula long-term fertilization experiment at the Smithsonian Tropical Research Institute in Panama, an ecosystem where P limitation constrains primary productivity and microbial activities. We monitored effects P addition on soil carbon decomposition with respiration measurements and investigated the responsible microbial mechanisms with metagenomics, metatranscriptomics, metaproteomics, and enzyme activity assays. We integrated the P dynamics into the C-N coupled Microbial Enzyme Decomposition (MEND) model. We integrated the `omics data with the new microbially-enabled C-N-P model to examine the mechanistic responses of soil microbial activity and heterotrophic respiration to P availability. Our finding indicates that increases in soil P availability can alter both the abundance and activity of enzymes related to soil carbon decomposition and P mineralization in the tropical soil, leading to increased CO2 emissions to the atmosphere. Integrating the `omics data into the biogeochemical model enabled scaling of complex ecosystem functions from genes to functional groups to enable predictions of microbial controls on C, N and P cycles.

  15. From nitrogen enrichment to oxygen depletion: a mechanistic model of coastal marine ecosystems response

    DEFF Research Database (Denmark)

    Cosme, Nuno Miguel Dias; Koski, Marja; Hauschild, Michael Zwicky

    oxygen (DO) consumption as a function of N input. Such indicator is the basis for an eXposure Factor (XF) applied in Life Cycle Impact Assessment (LCIA) to estimate impacts from N enrichment. The Large Marine Ecosystems (LME) biogeographical classification system was adopted to address the spatial......Nitrogen (N) emissions from anthropogenic sources may enrich coastal waters and lead to marine eutrophication impacts. Processes describing N-limited primary production (PP), zooplankton grazing, and bacterial respiration of sinking organic carbon, were modelled to quantify the potential dissolved...

  16. Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

    Directory of Open Access Journals (Sweden)

    B. Orcutt

    2008-11-01

    Full Text Available Anaerobic oxidation of methane (AOM is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007, none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

  17. Exposure factors for marine eutrophication impacts assessment based on a mechanistic biological model

    DEFF Research Database (Denmark)

    Cosme, Nuno Miguel Dias; Koski, Marja; Hauschild, Michael Zwicky

    2015-01-01

    routes from primary (cell aggregates) and secondary producers (faecal pellets, carcasses, and active vertical transport). Carbon export production (PE) and ecosystems eXposure Factors (XF), which represents a nitrogen-to-oxygen 'conversion' potential, were estimated at a spatial resolution of 66 large......Emissions of nitrogen (N) from anthropogenic sources enrich marine waters and promote planktonic growth. This newly synthesised organic carbon is eventually exported to benthic waters where aerobic respiration by heterotrophic bacteria results in the consumption of dissolved oxygen (DO......). This pathway is typical of marine eutrophication. A model is proposed to mechanistically estimate the response of coastal marine ecosystems to N inputs. It addresses the biological processes of nutrient-limited primary production (PP), metazoan consumption, and bacterial degradation, in four distinct sinking...

  18. Corrosion Prediction Model of Q235 Steel in Polluted Marine Atmospheric Environment

    Directory of Open Access Journals (Sweden)

    WANG Xu

    2017-04-01

    Full Text Available The corrosion behaviour of Q235 steel in Qingdao and Wanning of China,the two kinds of polluted marine environment were simulated by cyclic immersion test, and the correlation of indoor cyclic immersion test and outdoor marine atmospheric corrosion test of Q235 steel were studied. The corrosion morphologies, corrosion products, corrosion kinetics of Q235 steel were investigated with methods of scanning electron microscopy (SEM, X-ray diffraction (XRD and mass loss. The results reveal that the corrosion morphologies and compositions of corrosion products after cyclic immersion test agree with those after the real atmospheric test. Corrosion prediction model of Q235 steel in two kinds of marine atmospheric environment was built combined with Grey correlation method: T QD=137.002 t 1.093, T WN=102.398 t 0.952.

  19. Computer kinetic modelling of radionuclide accumulation in Marine organisms

    International Nuclear Information System (INIS)

    Quintella, H.M.; Santimateo, D.; Paschoa, A.S.

    1977-01-01

    Continuous System Modelling Program (CSMP) is used to simulate the first step of the kinetic of a radionuclide in a food chain by using the exponential model of accumulation from water-to-algae based on data found in the literature. The use of computer modelling as a tool for environmental studies is discussed as far as economical advantages and future applications are concerned

  20. Dynamic Model for Thrust Generation of Marine Propellers

    DEFF Research Database (Denmark)

    Blanke, Mogens; Lindegaard, Karl-Petter; Fossen, Thor I.

    2000-01-01

    Mathematical models of propeller thrust and torque are traditionally based on steady state thrust and torque characteristics obtained in model basin or cavitation tunnel tests. Experimental results showed that these quasi steady state models do not accurately describe the transient phenomena in a...

  1. Modeling aerosols and extinction in the marine atmospheric boundary layer

    NARCIS (Netherlands)

    Leeuw, G.; Eijk, A.M.; Noordhuis, G.R.

    1993-01-01

    An analysis is presented of aerosol particle size distributions measured over the North Atlantic and extinction coefficients derived from these data. Two empirical models, an aerosol model and an extinction model, are formulated in terms of simple meteorological parameters (wind speed, relative

  2. The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella

    Directory of Open Access Journals (Sweden)

    Julius Matthew L

    2011-05-01

    Full Text Available Abstract Background Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecology and evolution of diatoms in the world's oceans. Results The natural distribution of T. pseudonana spans both marine and fresh waters, and phylogenetic analyses of morphological and molecular datasets show that, 1 T. pseudonana marks an early divergence in a major freshwater radiation by diatoms, and 2 as a species, T. pseudonana is likely ancestrally freshwater. Marine strains therefore represent recent recolonizations of higher salinity habitats. In addition, the combination of a relatively nondescript form and a convoluted taxonomic history has introduced some confusion about the identity of T. pseudonana and, by extension, its phylogeny and ecology. We resolve these issues and use phylogenetic criteria to show that T. pseudonana is more appropriately classified by its original name, Cyclotella nana. Cyclotella contains a mix of marine and freshwater species and so more accurately conveys the complexities of the phylogenetic and natural histories of T. pseudonana. Conclusions The multitude of physical barriers that likely must be overcome for diatoms to successfully colonize freshwaters suggests that the physiological traits of T. pseudonana, and the genes underlying those traits, might differ from those of strictly marine diatoms. The freshwater ancestry of T. pseudonana might therefore confound generalizations about the physiological and metabolic properties of marine diatoms. The freshwater component of T. pseudonana's history merits careful consideration in the interpretation of experimental data collected for this important model species.

  3. 2011 Marine Hydrokinetic Device Modeling Workshop: Final Report; March 1, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Li, Y.; Reed, M.; Smith, B.

    2011-10-01

    This report summarizes the NREL Marine and Hydrokinetic Device Modeling Workshop. The objectives for the modeling workshop were to: (1) Review the designs of existing MHK device prototypes and discuss design and optimization procedures; (2) Assess the utility and limitations of modeling techniques and methods presently used for modeling MHK devices; (3) Assess the utility and limitations of modeling methods used in other areas, such as naval architecture and ocean engineering (e.g., oil & gas industry); and (4) Identify the necessary steps to link modeling with other important components that analyze MHK devices (e.g., tank testing, PTO design, mechanical design).

  4. Evaluation of Marine Corps Manpower Computer Simulation Model

    Science.gov (United States)

    2016-12-01

    overall end strength are maintained. To assist their mission, an agent-based computer simulation model was developed in the Java computer language...maintained. To assist their mission, an agent-based computer simulation model was developed in the Java computer language. This thesis investigates that...a simulation software that models business practices to assist that business in its “ability to analyze and make decisions on how to improve (their

  5. A hybrid finite difference and integral equation method for modeling and inversion of marine CSEM data

    DEFF Research Database (Denmark)

    Yoon, Daeung; Zhdanov, Michael; Cai, Hongzhu

    2015-01-01

    One of the major problems in the modeling and inversion of marine controlled source electromagnetic (MCSEM) data is related to the need for accurate representation of very complex geoelectrical models typical for marine environment. At the same time, the corresponding forward modeling algorithms...... should be powerful and fast enough to be suitable for repeated use in hundreds of iterations of the inversion and for multiple transmitter/receiver positions. To this end, we have developed a novel 3D modeling and inversion approach, which combines the advantages of the finite difference (FD......) and integral equation (IE) methods. In the framework of this approach, we solve the Maxwell's equations for anomalous electric fields using the FD approximation on a staggered grid. Once the unknown electric fields in the computation domain of the FD method are computed, the electric and magnetic fields...

  6. Optical modeling of aerosol extinction for remote sensing in the marine environment

    Science.gov (United States)

    Kaloshin, G. A.

    2013-05-01

    A microphysical model is presented for the surface layer marine and coastal atmospheric aerosols that is based on long-term observations of size distributions for 0.01-100 μm particles in different geographic sites. The fundamental feature of the model is a parameterization of amplitudes and widths for aerosol modes of the aerosol size distribution function (ASDF) as functions of fetch and wind speed. The shape of the ASDF and its dependence on meteorological parameters, altitudes above sea level (H), fetch (X), wind speed (U) and relative humidity (RH) are investigated. The spectral profiles of the aerosol extinction coefficients calculated by MaexPro (Marine Aerosol Extinction Profiles) are in good agreement with observational data and the numerical results obtained from the Navy Aerosol Model (NAM) and the Advanced Navy Aerosol Model (ANAM). Moreover, MaexPro was found to be an accurate and reliable tool for investigation of the optical properties of atmospheric aerosols.

  7. Modelling the distribution of a(w), pH and ions in marinated beef meat.

    Science.gov (United States)

    Lebert, André; Daudin, Jean-Dominique

    2014-07-01

    New beef products from low value cuts could be developed using marinating since this process has been shown to improve meat sensorial properties and shelf life. However, to optimise the process mathematical models are needed to predict evolution of the physicochemical properties that determine biochemical and structural changes. Two major works have been carried out to elaborate comprehensive models: (1) Thermodynamic models were adapted to predict water sorption isotherms and pH of beef meat tissue in presence of salts (NaCl, KCl) and organic acids (acetic, lactic, citric and ascorbic acid), (2) Fickian numerical models were set up to predict the migration of ions within meat cuts using apparent diffusivities previously estimated from 1D experiments. Simulation calculations showed reasonable agreement with measurements and can be used to investigate the effect of marinating conditions, product heterogeneity, dimension and shape. © 2013 Elsevier Ltd. All rights reserved.

  8. Evaluation model applied to TRANSPETRO's Marine Terminals Standardization Program

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Maria Fatima Ludovico de; Mueller, Gabriela [Pontificia Universidade Catolica do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ (Brazil). Instituto Tecnologico; Garcia, Luciano Maldonado [TRANSPETRO - PETROBRAS Transporte S.A., Rio de Janeiro, RJ (Brazil)

    2009-07-01

    This paper describes an innovative evaluation model applied to TRANSPETRO's 'Marine Terminals Standardization Program' based on updating approaches of programs evaluation and organizational learning. Since the program was launched in 2004, the need for having an evaluation model able to evaluate its implementation progress, to measure the degree of standards compliance and its potential economic, social and environmental impacts has become evident. Within a vision of safe and environmentally responsible operations of marine terminals, this evaluation model was jointly designed by TRANSPETRO and PUC-Rio to promote continuous improvement and learning in operational practices and in the standardization process itself. TRANSPETRO believes that standardization supports its services and management innovation capability by creating objective and internationally recognized parameters, targets and metrology for its business activities. The conceptual model and application guidelines for this important tool are presented in this paper, as well as the next steps towards its implementation. (author)

  9. Monitoring and Modeling Microbial Sulfate Reduction and Inhibition in a Mesoscale Tank Experiment

    Science.gov (United States)

    Hubbard, C. G.; Wu, Y.; Li, L.; Piceno, Y. M.; Cheng, Y.; Bill, M.; Coates, J. D.; Andersen, G. L.; Conrad, M. E.; Ajo Franklin, J. B.

    2014-12-01

    Subsurface biogeochemical cycling at the field-scale is controlled by a complex interplay between hydrological, geochemical and biological parameters. Mesoscale tank experiments can help to bridge the gap in complexity and understanding between well constrained batch and column experiments, and the interpretation of field data. In this contribution we present the results of a tank experiment investigating microbial sulfate reduction and inhibition in a porous media (20-30 mesh Ottawa sand). Microbial sulfate reduction is a process of wide biogeochemical significance, including in the context of oil reservoirs where the generation of sulfide can result in corrosion of steel infrastructure and additional downstream processing. Inhibition of sulfate reduction is therefore a high priority for this industry. Tracer experiments were conducted at the start and end of the experiment to constrain flow pathways and heterogeneities. The tank was inoculated with a San Francisco Bay mud/water enrichment utilizing acetate as the electron donor and continuous flow was initiated using bay-water with 10 mM acetate. Samples were taken from an array of 12 steel boreholes and showed spatiotemporal heterogeneities in the development of sulfidogenesis, reaching a peak of ~5 mM dissolved sulfide 71 days after inoculation. 10 mM perchlorate was then added to the influent to inhibit sulfidogenesis and dissolved sulfide decreased to ~0.03 mM by day 95. Stable isotope analysis of dissolved sulfate showed an increase in δ34S by ~10‰ compared with influent values but δ34S did not return to influent values by day 95, which may be indicative of the mixing between new and residual sulfate in the tank. Ongoing microbial community analyses are being used to help constrain microbial metabolisms. Finally, all the data is being integrated into a reactive transport model to better constrain the observed interplay between hydrology, geochemistry and biology.

  10. Modeling how soluble microbial products (SMP) support heterotrophic bacteria in autotroph-based biofilms

    DEFF Research Database (Denmark)

    Merkey, Brian; Rittmann, Bruce E.; Chopp, David L.

    2009-01-01

    . In this paper, we develop and use a mathematical model to describe a model biofilm system that includes autotrophic and heterotrophic bacteria and the key products produced by the bacteria. The model combines the methods of earlier multi-species models with a multi-component biofilm model in order to explore...... the interaction between species via exchange of soluble microbial products (SMP). We show that multiple parameter sets are able to describe the findings of experimental studies, and that heterotrophs growing on autotrophically produced SMP may pursue either r- or K-strategies to sustain themselves when SMP...... is their only substrate. We also show that heterotrophs can colonize some distance from the autotrophs and still be sustained by autotrophically produced SMP. This work defines the feasible range of parameters for utilization of SMP by heterotrophs and the nature of the interactions between autotrophs...

  11. Modelling marine sediment biogeochemistry: Current knowledge gaps, challenges, and some methodological advice for advancement

    DEFF Research Database (Denmark)

    Lessin, Gennadi; Artioli, Yuri; Almroth-Rosell, Elin

    2018-01-01

    -pronged approach for the advancement of benthic and benthic-pelagic modelling, essential for improved understanding, management and prediction of the marine environment. This includes: (A) Development of a traceable and hierarchical framework for benthic-pelagic models, which will facilitate integration among...... models, reduce risk of bias, and clarify model limitations; (B) extended cross-disciplinary approach to promote effective collaboration between modelling and empirical scientists of various backgrounds and better involvement of stakeholders and end-users; (C) a common vocabulary for terminology used...

  12. A Marine Dispersion Model for Radionuclides and its Calibration from Non Radiological Information

    Science.gov (United States)

    Abril, J. M.; GarcíA-León, M.

    A realistic assesment of public exposure to man-made radionuclides released into the marine environment requires specific long term transport models. Here we present some developments on a standard model that could be applied even to marine scenarios of which no previous radiological history exists. Under certain general assumptions advenction and diffusion are described by a transfer equation. The transfer coefficients are found, consequently, as functions of the grid-cell geometry and water movements. A mathematical development and a first validation of our model are briefly reported. Testing of the model has been done in the Irish Sea. It was totally covered by a grid 5.16 km of typical dimensions. The time step was of 1.75 hours in order to keep a low numerical dispersion. Batimetry has been readen from marine charts and the advenctive part of transfer coefficients was evaluated by using a residual stream function. Diffusional part of such coefficients were formulated reflecting the Shear effect as well as the remaining turbulent diffusion. Calibration of this formulation has been carried out by modelling the salinity distribution in the Irish Sea. For that, it has been a decisive task modelling the dispersion of river discharges as well as the net balance of evaporation-precipitation. The calibrate transfer coefficients are then used to simulate the dispersion of the 137Cs released by Sellafield. Some preliminary results are shown and discussed.

  13. Model description of trophodynamic behavior of methylmercury in a marine aquatic system

    International Nuclear Information System (INIS)

    Tong Yindong; Zhang Wei; Hu Xindi; Ou Langbo; Hu Dan; Yang Tianjun; Wei Wen; Wang Xuejun

    2012-01-01

    A marine food web in Bohai Bay, China, was selected to study methylmercury (MeHg) bioaccumulation, and an aquivalence-based mass balance model was established to explore the possibility of predicting the MeHg concentrations and quantifying MeHg bioaccumulation in the food web. Results showed that both total mercury (THg) and MeHg were biomagnified in the food web. The calculated MeHg concentrations in the selected species agreed well with the measured values, which shows the model could be a useful tool in MeHg concentration prediction in food web. Model outputs also showed that metabolism and growth dilution could be the dominant mechanisms for the reduction of MeHg levels in aquatic organisms. With the increase of trophic level, the contribution of food as a MeHg source for organism is increasing, and MeHg from prey was the dominant source. - Highlights: ► We model the bioaccumulation of methylmercury in a marine aquatic food web. ► Aquivalence-based mass balance model could quantify MeHg trophic transfer. ► Metabolism and growth dilution are dominant mechanisms of MeHg reduction in organisms. ► With increase of trophic levels, contribution of food as MeHg source is increasing. - Aquivalence-based mass balance model was established to study methylmercury bioaccumulation in a marine food web.

  14. Practical applications of the multi-component marine photosynthesis model (MCM

    Directory of Open Access Journals (Sweden)

    Dariusz Ficek

    2003-09-01

    Full Text Available This paper describes the applications and accuracy analyses of our multi-component model of marine photosynthesis, given in detail in Woźniak et al. (2003. We now describe an application of the model to determine quantities characterising the photosynthesis of marine algae, especially the quantum yield of photosynthesis and photosynthetic primary production. These calculations have permitted the analysis of the variability of these photosynthesis characteristics in a diversity of seas, at different seasons, and at different depths. Because of its structure, the model can be used as the "marine part" of break a "satellite" algorithm for monitoring primary production in the sea (the set of input data necessary for the calculations can be determined with remote sensing methods. With this in mind, in the present work, we have tested and verified the model using empirical data. The verification yielded satisfactory results: for example, the statistical errors in estimates of primary production in the water column for Case 1 Waters do not exceed 45%. Hence, this model is far more accurate than earlier, less complex models hitherto applied in satellite algorithms.

  15. Model-based Control of a Bottom Fired Marine Boiler

    DEFF Research Database (Denmark)

    Solberg, Brian; Karstensen, Claus M. S.; Andersen, Palle

    This paper focuses on applying model based MIMO control to minimize variations in water level for a specific boiler type. A first principles model is put up. The model is linearized and an LQG controller is designed. Furthermore the benefit of using a steam °ow measurement is compared to a strategy...... relying on estimates of the disturbance. Preliminary tests at the boiler system show that the designed controller is able to control the boiler process. Furthermore it can be concluded that relying on estimates of the steam flow in the control strategy does not decrease the controller performance...

  16. Model-based Control of a Bottom Fired Marine Boiler

    DEFF Research Database (Denmark)

    Solberg, Brian; Karstensen, Claus M. S.; Andersen, Palle

    2005-01-01

    This paper focuses on applying model based MIMO control to minimize variations in water level for a specific boiler type. A first principles model is put up. The model is linearized and an LQG controller is designed. Furthermore the benefit of using a steam °ow measurement is compared to a strategy...... relying on estimates of the disturbance. Preliminary tests at the boiler system show that the designed controller is able to control the boiler process. Furthermore it can be concluded that relying on estimates of the steam flow in the control strategy does not decrease the controller performance...

  17. Research on marine and freshwater fish identification model based on hyper-spectral imaging technology

    Science.gov (United States)

    Fu, Yan; Guo, Pei-yuan; Xiang, Ling-zi; Bao, Man; Chen, Xing-hai

    2013-08-01

    With the gradually mature of hyper spectral image technology, the application of the meat nondestructive detection and recognition has become one of the current research focuses. This paper for the study of marine and freshwater fish by the pre-processing and feature extraction of the collected spectral curve data, combined with BP network structure and LVQ network structure, a predictive model of hyper spectral image data of marine and freshwater fish has been initially established and finally realized the qualitative analysis and identification of marine and freshwater fish quality. The results of this study show that hyper spectral imaging technology combined with the BP and LVQ Artificial Neural Network Model can be used for the identification of marine and freshwater fish detection. Hyper-spectral data acquisition can be carried out without any pretreatment of the samples, thus hyper-spectral imaging technique is the lossless, high- accuracy and rapid detection method for quality of fish. In this study, only 30 samples are used for the exploratory qualitative identification of research, although the ideal study results are achieved, we will further increase the sample capacity to take the analysis of quantitative identification and verify the feasibility of this theory.

  18. A general-purpose process modelling framework for marine energy systems

    International Nuclear Information System (INIS)

    Dimopoulos, George G.; Georgopoulou, Chariklia A.; Stefanatos, Iason C.; Zymaris, Alexandros S.; Kakalis, Nikolaos M.P.

    2014-01-01

    Highlights: • Process modelling techniques applied in marine engineering. • Systems engineering approaches to manage the complexity of modern ship machinery. • General purpose modelling framework called COSSMOS. • Mathematical modelling of conservation equations and related chemical – transport phenomena. • Generic library of ship machinery component models. - Abstract: High fuel prices, environmental regulations and current shipping market conditions impose ships to operate in a more efficient and greener way. These drivers lead to the introduction of new technologies, fuels, and operations, increasing the complexity of modern ship energy systems. As a means to manage this complexity, in this paper we present the introduction of systems engineering methodologies in marine engineering via the development of a general-purpose process modelling framework for ships named as DNV COSSMOS. Shifting the focus from components – the standard approach in shipping- to systems, widens the space for optimal design and operation solutions. The associated computer implementation of COSSMOS is a platform that models, simulates and optimises integrated marine energy systems with respect to energy efficiency, emissions, safety/reliability and costs, under both steady-state and dynamic conditions. DNV COSSMOS can be used in assessment and optimisation of design and operation problems in existing vessels, new builds as well as new technologies. The main features and our modelling approach are presented and key capabilities are illustrated via two studies on the thermo-economic design and operation optimisation of a combined cycle system for large bulk carriers, and the transient operation simulation of an electric marine propulsion system

  19. SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

    Science.gov (United States)

    Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

    2015-08-01

    SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass, and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently

  20. A protocol for the intercomparison of marine fishery and ecosystem models: Fish-MIP v1.0

    Science.gov (United States)

    Tittensor, Derek P.; Eddy, Tyler D.; Lotze, Heike K.; Galbraith, Eric D.; Cheung, William; Barange, Manuel; Blanchard, Julia L.; Bopp, Laurent; Bryndum-Buchholz, Andrea; Büchner, Matthias; Bulman, Catherine; Carozza, David A.; Christensen, Villy; Coll, Marta; Dunne, John P.; Fernandes, Jose A.; Fulton, Elizabeth A.; Hobday, Alistair J.; Huber, Veronika; Jennings, Simon; Jones, Miranda; Lehodey, Patrick; Link, Jason S.; Mackinson, Steve; Maury, Olivier; Niiranen, Susa; Oliveros-Ramos, Ricardo; Roy, Tilla; Schewe, Jacob; Shin, Yunne-Jai; Silva, Tiago; Stock, Charles A.; Steenbeek, Jeroen; Underwood, Philip J.; Volkholz, Jan; Watson, James R.; Walker, Nicola D.

    2018-04-01

    Model intercomparison studies in the climate and Earth sciences communities have been crucial to building credibility and coherence for future projections. They have quantified variability among models, spurred model development, contrasted within- and among-model uncertainty, assessed model fits to historical data, and provided ensemble projections of future change under specified scenarios. Given the speed and magnitude of anthropogenic change in the marine environment and the consequent effects on food security, biodiversity, marine industries, and society, the time is ripe for similar comparisons among models of fisheries and marine ecosystems. Here, we describe the Fisheries and Marine Ecosystem Model Intercomparison Project protocol version 1.0 (Fish-MIP v1.0), part of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP), which is a cross-sectoral network of climate impact modellers. Given the complexity of the marine ecosystem, this class of models has substantial heterogeneity of purpose, scope, theoretical underpinning, processes considered, parameterizations, resolution (grain size), and spatial extent. This heterogeneity reflects the lack of a unified understanding of the marine ecosystem and implies that the assemblage of all models is more likely to include a greater number of relevant processes than any single model. The current Fish-MIP protocol is designed to allow these heterogeneous models to be forced with common Earth System Model (ESM) Coupled Model Intercomparison Project Phase 5 (CMIP5) outputs under prescribed scenarios for historic (from the 1950s) and future (to 2100) time periods; it will be adapted to CMIP phase 6 (CMIP6) in future iterations. It also describes a standardized set of outputs for each participating Fish-MIP model to produce. This enables the broad characterization of differences between and uncertainties within models and projections when assessing climate and fisheries impacts on marine ecosystems and the

  1. A protocol for the intercomparison of marine fishery and ecosystem models: Fish-MIP v1.0

    Directory of Open Access Journals (Sweden)

    D. P. Tittensor

    2018-04-01

    Full Text Available Model intercomparison studies in the climate and Earth sciences communities have been crucial to building credibility and coherence for future projections. They have quantified variability among models, spurred model development, contrasted within- and among-model uncertainty, assessed model fits to historical data, and provided ensemble projections of future change under specified scenarios. Given the speed and magnitude of anthropogenic change in the marine environment and the consequent effects on food security, biodiversity, marine industries, and society, the time is ripe for similar comparisons among models of fisheries and marine ecosystems. Here, we describe the Fisheries and Marine Ecosystem Model Intercomparison Project protocol version 1.0 (Fish-MIP v1.0, part of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP, which is a cross-sectoral network of climate impact modellers. Given the complexity of the marine ecosystem, this class of models has substantial heterogeneity of purpose, scope, theoretical underpinning, processes considered, parameterizations, resolution (grain size, and spatial extent. This heterogeneity reflects the lack of a unified understanding of the marine ecosystem and implies that the assemblage of all models is more likely to include a greater number of relevant processes than any single model. The current Fish-MIP protocol is designed to allow these heterogeneous models to be forced with common Earth System Model (ESM Coupled Model Intercomparison Project Phase 5 (CMIP5 outputs under prescribed scenarios for historic (from the 1950s and future (to 2100 time periods; it will be adapted to CMIP phase 6 (CMIP6 in future iterations. It also describes a standardized set of outputs for each participating Fish-MIP model to produce. This enables the broad characterization of differences between and uncertainties within models and projections when assessing climate and fisheries impacts on marine ecosystems

  2. Modeling of decomposition activity and priming effect in soil using the versatile index of microbial physiological state

    Science.gov (United States)

    Blagodatskiy, Sergey

    2015-04-01

    The implementation of microbial biomass in soil organic matter (SOM) models is still unresolved issue. The approaches using explicit description of microbial biomass (decomposer) interaction with SOM usually cannot be easily verified by means of experimental estimating of total microbial biomass dynamics. Standard experimental methods, such as fumigation extraction or direct microscopic count, does not represent microbial activity (Blagodatskaya and Kuzyakov, 2013), which is essential for the control of decomposition rate. More advanced approaches, explicitly simulating intracellular metabolic activity (Resat et al., 2012) and e.g. production and turnover of extracellular enzymes (Lawrence et al., 2009) are prohibitively complex for the field and larger scales, which are most often under demand for SOM modelling. One possible parsimonious solution is an application of index of microbial physiological state (r), which describes the adaptive variation of the cell composition and metabolic activity by one variable (Panikov, 1995). This variable (r) can reflect the microbial response to the availability of carbon and nitrogen and shift of microbial biomass between active and dormant state (Blagodatsky and Richter, 1998), but also can be used for the description of the effect of external factors, such as temperature and moisture, on microbial activity. This approach is extremely useful for the description of priming effect (Blagodatsky et al., 2010) and the influence of substrate availability and external factors on the size and dynamics of priming. Distinguishing of these two types of driving forces for priming is crucial for modelling of SOM dynamics and steady-state stocks of different SOM pools. I will present the analysis of model response on combination of limiting factors presented as functions controlling the change of microbial physiological state and size of priming effect. Alternatively, the direct effect of the same factors on decomposition rate and priming

  3. Modeling Marine Exposure to Polychlorinated Biphenyls from Sunken Ships.

    Science.gov (United States)

    1996-12-01

    shoulders, he still carried me faithfully and tirelessly on his. And for riding coach and now fiancee, Ms. Kelley Anne McCarty, who understands...C Vsc =64.03(m 3) The model recalculates the volume of all trophic levels every time step. PCBs enter the food chain at the lowest levels through

  4. Validation of an Eulerian population model for the marine copepod Calanus finmarchicus in the Norwegian Sea

    Science.gov (United States)

    Alver, Morten Omholt; Broch, Ole Jacob; Melle, Webjørn; Bagøien, Espen; Slagstad, Dag

    2016-08-01

    Calanus finmarchicus is an important zooplankton species in the Norwegian Sea, as a dominant food organism for pelagic fish larvae, and a potentially large source of marine lipids and proteins. Its position in the marine food web also makes it an important model species in assessing the risk posed by oil spills in the Norwegian and Arctic Seas. In this study, an Eulerian population model for C.finmarchicus, coupled to the physical and ecological model SINMOD, is presented. The model includes the full life cycle of C. finmarchicus with a representation of all developmental stages. The model has been validated against field measurements made in different areas of the Norwegian Sea in 1997 and 1998. The model displays geographical and temporal distributions of development stages that is in line with observed patterns. When comparing time series for selected regions, we see a high degree of variability both in the field samples and model output. On average, the model deviations are near half of the summed variability of the field data and model estimates. The model has applications within assessment of ecological production, and the potential for harvesting in the Norwegian and Arctic Seas, but in combination with other models, also for the assessment of ecological effects of oil spills and other types of pollution.

  5. A model marine-science curriculum for fourth-grade pupils in Florida

    Science.gov (United States)

    Schulte, Philip James

    This dissertation focused on the development of a model marine-science curriculum for fourth-grade pupils in the State of Florida. The curriculum was developed using grounded theory research method, including a component of data collected from an on-line survey administered to 106 professional educators and marine biologists. The results of the data collection and analysis showed a definitive necessity for teacher preparedness, multidisciplinary content, and inquiry-based science instruction. Further, three important factors emerged: (a) collaborative grouping increases achievement; (b) field excursions significantly impact student motivation; (c) standardized testing influences curriculum development. The curriculum is organized as an 11-day unit, with detailed lesson plans presented in standard curricular format and with all components correlated to the Florida State Educational Standards. The curriculum incorporates teacher preparation, multimedia presentations, computer-assisted instruction, scientific art appreciation, and replication as well as assessment factors. The curriculum addresses topics of ichthyology, marine animal identification, environmental conservation and protection, marine animal anatomy, water safety, environmental stewardship, and responsible angling techniques. The components of the curriculum were discussed with reference to the literature on which it was based and recommendations for future research were addressed.

  6. Marine denitrification rates determined from a global 3-D inverse model

    Directory of Open Access Journals (Sweden)

    T. DeVries

    2013-04-01

    Full Text Available A major impediment to understanding long-term changes in the marine nitrogen (N cycle is the persistent uncertainty about the rates, distribution, and sensitivity of its largest fluxes in the modern ocean. We use a global ocean circulation model to obtain the first 3-D estimate of marine denitrification rates that is maximally consistent with available observations of nitrate deficits and the nitrogen isotopic ratio of oceanic nitrate. We find a global rate of marine denitrification in suboxic waters and sediments of 120–240 Tg N yr−1, which is lower than many other recent estimates. The difference stems from the ability to represent the 3-D spatial structure of suboxic zones, where denitrification rates of 50–77 Tg N yr−1 result in up to 50% depletion of nitrate. This depletion reduces the effect of local isotopic enrichment on the rest of the ocean, allowing the N isotope ratio of oceanic nitrate to be achieved with a sedimentary denitrification rate about 1.3–2.3 times that of suboxic zones. This balance of N losses between sediments and suboxic zones is shown to obey a simple relationship between isotope fractionation and the degree of nitrate consumption in the core of the suboxic zones. The global denitrification rates derived here suggest that the marine nitrogen budget is likely close to balanced.

  7. A mechanistic soil biogeochemistry model with explicit representation of microbial and macrofaunal activities and nutrient cycles

    Science.gov (United States)

    Fatichi, Simone; Manzoni, Stefano; Or, Dani; Paschalis, Athanasios

    2016-04-01

    The potential of a given ecosystem to store and release carbon is inherently linked to soil biogeochemical processes. These processes are deeply connected to the water, energy, and vegetation dynamics above and belowground. Recently, it has been advocated that a mechanistic representation of soil biogeochemistry require: (i) partitioning of soil organic carbon (SOC) pools according to their functional role; (ii) an explicit representation of microbial dynamics; (iii) coupling of carbon and nutrient cycles. While some of these components have been introduced in specialized models, they have been rarely implemented in terrestrial biosphere models and tested in real cases. In this study, we combine a new soil biogeochemistry model with an existing model of land-surface hydrology and vegetation dynamics (T&C). Specifically the soil biogeochemistry component explicitly separates different litter pools and distinguishes SOC in particulate, dissolved and mineral associated fractions. Extracellular enzymes and microbial pools are explicitly represented differentiating the functional roles of bacteria, saprotrophic and mycorrhizal fungi. Microbial activity depends on temperature, soil moisture and litter or SOC stoichiometry. The activity of macrofauna is also modeled. Nutrient dynamics include the cycles of nitrogen, phosphorous and potassium. The model accounts for feedbacks between nutrient limitations and plant growth as well as for plant stoichiometric flexibility. In turn, litter input is a function of the simulated vegetation dynamics. Root exudation and export to mycorrhiza are computed based on a nutrient uptake cost function. The combined model is tested to reproduce respiration dynamics and nitrogen cycle in few sites where data were available to test plausibility of results across a range of different metrics. For instance in a Swiss grassland ecosystem, fine root, bacteria, fungal and macrofaunal respiration account for 40%, 23%, 33% and 4% of total belowground

  8. Application of oil spill model to marine pollution and risk control problems

    Science.gov (United States)

    Aseev, Nikita; Agoshkov, Valery; Sheloput, Tatyana

    2017-04-01

    Oil transportation by sea induces challenging problems of environmental control. Millions of tonnes of oil are yearly released during routine ship operations, not to mention vast spills due to different accidents (e.g. tanker collisions, grounding, etc.). Oil pollution is dangerous to marine organisms such as plants, fish and mammals, leading to widespread damage to our planet. In turn, fishery and travel agencies can lose money and clients, and ship operators are obliged to pay huge penalties for environmental pollution. In this work we present the method of accessing oil pollution of marine environment using recently developed oil spill model. The model describes basic processes of the oil slick evolution: oil transport due to currents, drift under the action of wind, spreading on the surface, evaporation, emulsification and dispersion. Such parameters as slick location, mass, density of oil, water content, viscosity and density of "water-in-oil" emulsion can be calculated. We demonstrate how to apply the model to damage calculation problems using a concept of average damage to particular marine area. We also formulate the problem of oil spill risk control, when some accident parameters are not known, but their probability distribution is given. We propose a new algorithm to solve such problems and show results of our model simulations. The work can be interesting to broad environmental, physics and mathematics community. The work is supported by Russian Foundation for Basic Research grant 16-31-00510.

  9. A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

    Directory of Open Access Journals (Sweden)

    Acácio A. Navarrete

    2010-05-01

    Full Text Available The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production.The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I—“Slash-and-Burn” the community structures detected by automated ribosomal intergenic spacer analysis (ARISA revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II—“Anthropogenic Soil”, the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP differed among an Amazonian Dark Earth (ADE, black carbon (BC and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria—24% ADE, 15% BC; Acidobacteria—10% ADE, 21% BC; Actinobacteria—7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes—3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the

  10. Coupling ecosystems exposure to nitrogen and species sensitivity to hypoxia: modelling marine eutrophication in LCIA

    DEFF Research Database (Denmark)

    Cosme, Nuno Miguel Dias; Koski, Marja; Hauschild, Michael Zwicky

    Characterisation modelling in Life Cycle Impact Assessment (LCIA) quantifies impacts of anthropogenic emissions by applying substance-specific impact potentials, or Characterisation Factors (CF), to the amount of substances emitted. Nitrogen (N) emissions from human activities enrich coastal marine...... ecosystems and promote planktonic growth that may lead to marine eutrophication impacts. Excessive algal biomass and dissolved oxygen (DO) depletion typify the ecosystem response to the nutrient input. The present novel method couples a mechanistic model of coastal biological processes that determines...... the ecosystem response (exposure) to anthropogenic N enrichment (eXposure Factor, XF [kgO2·kgN-1]) with the sensitivity of species exposed to oxygen-depleted waters (Effect Factor, EF [(PAF)·m3·kgO2-1], expressed as a Potentially Affected Fraction (PAF) of species). Thus, the coupled indicator (XF*EF, [(PAF)·m3...

  11. Waste production and regional growth of marine activities an econometric model.

    Science.gov (United States)

    Bramati, Maria Caterina

    2016-11-15

    Coastal regions are characterized by intense human activity and climatic pressures, often intensified by competing interests in the use of marine waters. To assess the effect of public spending on the regional economy, an econometric model is here proposed. Not only are the regional investment and the climatic risks included in the model, but also variables related to the anthropogenic pressure, such as population, economic activities and waste production. Feedback effects of economic and demographic expansion on the pollution of coastal areas are also considered. It is found that dangerous waste increases with growing shipping and transportation activities and with growing population density in non-touristic coastal areas. On the other hand, the amount of non-dangerous wastes increases with marine mining, defense and offshore energy production activities. However, lower waste production occurs in areas where aquaculture and touristic industry are more exploited, and accompanied by increasing regional investment in waste disposal. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Bayesian analysis of non-linear differential equation models with application to a gut microbial ecosystem.

    Science.gov (United States)

    Lawson, Daniel J; Holtrop, Grietje; Flint, Harry

    2011-07-01

    Process models specified by non-linear dynamic differential equations contain many parameters, which often must be inferred from a limited amount of data. We discuss a hierarchical Bayesian approach combining data from multiple related experiments in a meaningful way, which permits more powerful inference than treating each experiment as independent. The approach is illustrated with a simulation study and example data from experiments replicating the aspects of the human gut microbial ecosystem. A predictive model is obtained that contains prediction uncertainty caused by uncertainty in the parameters, and we extend the model to capture situations of interest that cannot easily be studied experimentally. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Analysis of trait-based models in marine ecosystems

    DEFF Research Database (Denmark)

    Heilmann, Irene Louise Torpe

    -temporal pattern formation in a predator–prey system where animals move towards higher fitness. Reaction-diffusion systems have been used extensively to describe spatio-temporal patterns in a variety of systems. However, animals rarely move completely at random, as expressed by diffusion. This has lead to models...... with taxis terms, describing individuals moving in the direction of an attractant. An example is chemotaxis models, where bacteria are attracted to a chemical substance. From an evolutionary perspective, it is expected that animals act as to optimize their fitness. Based on this principle, a predator......–prey system with fitness taxis and diffusion is proposed. Here, fitness taxis refer to animals moving towards higher values of fitness, and the specific growth rates of the populations are used as a measure of the fitness values. To determine the conditions for pattern formation, a linear stability analysis...

  14. Stoichiometry constrains microbial response to root exudation- insights from a model and a field experiment in a temperate forest

    Science.gov (United States)

    Drake, J. E.; Darby, B. A.; Giasson, M.-A.; Kramer, M. A.; Phillips, R. P.; Finzi, A. C.

    2013-02-01

    Plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exoenzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The nitrogen (N) content of microbial biomass and exoenzymes may introduce a stoichiometric constraint on the ability of microbes to effectively utilize the root exudates, particularly if the exudates are rich in C but low in N. We combined a theoretical model of microbial activity with an exudation experiment to test the hypothesis that the ability of soil microbes to utilize root exudates for the synthesis of additional biomass and exoenzymes is constrained by N availability. The field experiment simulated exudation by automatically pumping solutions of chemicals often found in root exudates ("exudate mimics") containing C alone or C in combination with N (C : N ratio of 10) through microlysimeter "root simulators" into intact forest soils in two 50-day experiments. The delivery of C-only exudate mimics increased microbial respiration but had no effect on microbial biomass or exoenzyme activities. By contrast, experimental delivery of exudate mimics containing both C and N significantly increased microbial respiration, microbial biomass, and the activity of exoenzymes that decompose low molecular weight components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exoenzymes that degrade high molecular weight SOM (e.g., polyphenols, lignin). The modeling results were consistent with the experiments; simulated delivery of C-only exudates induced microbial N-limitation, which constrained the synthesis of microbial biomass and exoenzymes. Exuding N as well as C alleviated this stoichiometric constraint in the model, allowing for increased exoenzyme production, the priming of decomposition, and a net release of N from SOM (i

  15. Stoichiometry constrains microbial response to root exudation- insights from a model and a field experiment in a temperate forest

    Directory of Open Access Journals (Sweden)

    J. E. Drake

    2013-02-01

    Full Text Available Plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exoenzymes they synthesize, leading to accelerated rates of carbon (C mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The nitrogen (N content of microbial biomass and exoenzymes may introduce a stoichiometric constraint on the ability of microbes to effectively utilize the root exudates, particularly if the exudates are rich in C but low in N. We combined a theoretical model of microbial activity with an exudation experiment to test the hypothesis that the ability of soil microbes to utilize root exudates for the synthesis of additional biomass and exoenzymes is constrained by N availability. The field experiment simulated exudation by automatically pumping solutions of chemicals often found in root exudates ("exudate mimics" containing C alone or C in combination with N (C : N ratio of 10 through microlysimeter "root simulators" into intact forest soils in two 50-day experiments. The delivery of C-only exudate mimics increased microbial respiration but had no effect on microbial biomass or exoenzyme activities. By contrast, experimental delivery of exudate mimics containing both C and N significantly increased microbial respiration, microbial biomass, and the activity of exoenzymes that decompose low molecular weight components of soil organic matter (SOM, e.g., cellulose, amino sugars, while decreasing the activity of exoenzymes that degrade high molecular weight SOM (e.g., polyphenols, lignin. The modeling results were consistent with the experiments; simulated delivery of C-only exudates induced microbial N-limitation, which constrained the synthesis of microbial biomass and exoenzymes. Exuding N as well as C alleviated this stoichiometric constraint in the model, allowing for increased exoenzyme production, the priming of decomposition, and a net release of N

  16. A Systematic Review of Marine-Based Species Distribution Models (SDMs with Recommendations for Best Practice

    Directory of Open Access Journals (Sweden)

    Néstor M. Robinson

    2017-12-01

    Full Text Available In the marine environment Species Distribution Models (SDMs have been used in hundreds of papers for predicting the present and future geographic range and environmental niche of species. We have analyzed ways in which SDMs are being applied to marine species in order to recommend best practice in future studies. This systematic review was registered as a protocol on the Open Science Framework: https://osf.io/tngs6/. The literature reviewed (236 papers was published between 1992 and July 2016. The number of papers significantly increased through time (R2 = 0.92, p < 0.05. The studies were predominantly carried out in the Temperate Northern Atlantic (45% followed by studies of global scale (11% and studies in Temperate Australasia (10%. The majority of studies reviewed focused on theoretical ecology (37% including investigations of biological invasions by non-native organisms, conservation planning (19%, and climate change predictions (17%. Most of the studies were published in ecological, multidisciplinary, or biodiversity conservation journals. Most of the studies (94% failed to report the amount of uncertainty derived from data deficiencies and model parameters. Best practice recommendations are proposed here to ensure that novice and advanced SDM users can (a understand the main elements of SDMs, (b reproduce standard methods and analysis, and (c identify potential limitations with their data. We suggest that in the future, studies of marine SDMs should report on key features of the approaches employed, data deficiencies, the selection of the best explanatory model, and the approach taken to validate the SDM results. In addition, based on the literature reviewed, we suggest that future marine SDMs should account for uncertainty levels as part of the modeling process.

  17. Porphyromonas gingivalis and Treponema denticola Mixed Microbial Infection in a Rat Model of Periodontal Disease

    Directory of Open Access Journals (Sweden)

    Raj K. Verma

    2010-01-01

    Full Text Available Porphyromonas gingivalis and Treponema denticola are periodontal pathogens that express virulence factors associated with the pathogenesis of periodontitis. In this paper we tested the hypothesis that P. gingivalis and T. denticola are synergistic in terms of virulence; using a model of mixed microbial infection in rats. Groups of rats were orally infected with either P. gingivalis or T. denticola or mixed microbial infections for 7 and 12 weeks. P. gingivalis genomic DNA was detected more frequently by PCR than T. denticola. Both bacteria induced significantly high IgG, IgG2b, IgG1, IgG2a antibody levels indicating a stimulation of Th1 and Th2 immune response. Radiographic and morphometric measurements demonstrated that rats infected with the mixed infection exhibited significantly more alveolar bone loss than shaminfected control rats. Histology revealed apical migration of junctional epithelium, rete ridge elongation, and crestal alveolar bone resorption; resembling periodontal disease lesion. These results showed that P. gingivalis and T. denticola exhibit no synergistic virulence in a rat model of periodontal disease.

  18. Marine Mammal Brucella Reference Strains Are Attenuated in a BALB/c Mouse Model.

    Science.gov (United States)

    Nymo, Ingebjørg H; Arias, Maykel A; Pardo, Julián; Álvarez, María Pilar; Alcaraz, Ana; Godfroid, Jacques; Jiménez de Bagüés, María Pilar

    2016-01-01

    Brucellosis is a zoonosis of worldwide distribution with numerous animal host species. Since the novel isolation of Brucella spp. from marine mammals in 1994 the bacteria have been isolated from various marine mammal hosts. The marine mammal reference strains Brucella pinnipedialis 12890 (harbour seal, Phoca vitulina) and Brucella ceti 12891 (harbour porpoise, Phocoena phocoena) were included in genus Brucella in 2007, however, their pathogenicity in the mouse model is pending. Herein this is evaluated in BALB/c mice with Brucella suis 1330 as a control. Both marine mammal strains were attenuated, however, B. ceti was present at higher levels than B. pinnipedialis in blood, spleen and liver throughout the infection, in addition B. suis and B. ceti were isolated from brains and faeces at times with high levels of bacteraemia. In B. suis-infected mice serum cytokines peaked at day 7. In B. pinnipedialis-infected mice, levels were similar, but peaked predominantly at day 3 and an earlier peak in spleen weight likewise implied an earlier response. The inflammatory response induced pathology in the spleen and liver. In B. ceti-infected mice, most serum cytokine levels were comparable to those in uninfected mice, consistent with a limited inflammatory response, which also was indicated by restricted spleen and liver pathology. Specific immune responses against all three strains were detected in vitro after stimulation of splenocytes from infected mice with the homologous heat-killed brucellae. Antibody responses in vivo were also induced by the three brucellae. The immunological pattern of B. ceti in combination with persistence in organs and limited pathology has heretofore not been described for other brucellae. These two marine mammal wildtype strains show an attenuated pattern in BALB/c mice only previously described for Brucella neotomea.

  19. Implementation of marine halogen chemistry into the Community Multiscale Air Quality (CMAQ) model

    Science.gov (United States)

    Gantt, B.; Sarwar, G.

    2017-12-01

    In two recent studies (Sarwar et al, 2015 and Gantt et al., 2017), the impact of marine halogen (bromine and iodine) chemistry on air quality has been evaluated using the Community Multiscale Air Quality (CMAQ) model. We found that marine halogen chemistry not only has the expected effect of reducing marine boundary layer ozone concentrations, but also reduces ozone in the free troposphere and inland from the coast. In Sarwar et al. (2015), the impact of the halogen chemistry without and with photochemical reactions of higher iodine oxides over the Northern Hemisphere was examined using the coarse horizontal grids of a hemispheric domain. Halogen chemistry without and with the photochemical reactions of higher iodine oxides reduces ozone over seawater by 15% and 48%, respectively. Using the results of the chemistry without the photochemical reactions of higher iodine oxides, we developed a simple first order ozone loss rate and implemented it into the public version of CMAQv52. In Gantt et al. (2017), the impact of the simple first order loss rate as well as the full halogen chemistry without photochemical reactions of higher iodine oxides over the continental United States was examined using finer horizontal grids of the regional domain and boundary conditions from the hemispheric domain with and without marine halogen chemistry. The boundary conditions obtained with the halogen chemistry as well as the simple halogen chemistry reduces ozone along the coast where CMAQ typically overpredicts the concentrations. Development of halogen chemistry in CMAQ has continued with the implementation of several heterogeneous reactions of bromine and iodine species, revised reactions of higher iodine oxides, and a refined marine halogen emissions inventory. Our latest version of halogen chemistry with photochemical reactions of higher iodine oxides reduces ozone by 23% over the seawater. This presentation will discuss the previous and ongoing implementation of revised halogen

  20. Marine productivity response to Heinrich events: a model-data comparison

    CSIR Research Space (South Africa)

    Mariotti, V

    2012-10-01

    Full Text Available Marine sediments records suggest large changes in marine productivity during glacial periods, with abrupt variations especially during the Heinrich events. Here, we study the response of marine biogeochemistry to such an event by using a...

  1. Application of the perfectly matched layer in 3-D marine controlled-source electromagnetic modelling

    Science.gov (United States)

    Li, Gang; Li, Yuguo; Han, Bo; Liu, Zhan

    2018-01-01

    In this study, the complex frequency-shifted perfectly matched layer (CFS-PML) in stretching Cartesian coordinates is successfully applied to 3-D frequency-domain marine controlled-source electromagnetic (CSEM) field modelling. The Dirichlet boundary, which is usually used within the traditional framework of EM modelling algorithms, assumes that the electric or magnetic field values are zero at the boundaries. This requires the boundaries to be sufficiently far away from the area of interest. To mitigate the boundary artefacts, a large modelling area may be necessary even though cell sizes are allowed to grow toward the boundaries due to the diffusion of the electromagnetic wave propagation. Compared with the conventional Dirichlet boundary, the PML boundary is preferred as the modelling area of interest could be restricted to the target region and only a few absorbing layers surrounding can effectively depress the artificial boundary effect without losing the numerical accuracy. Furthermore, for joint inversion of seismic and marine CSEM data, if we use the PML for CSEM field simulation instead of the conventional Dirichlet, the modelling area for these two different geophysical data collected from the same survey area could be the same, which is convenient for joint inversion grid matching. We apply the CFS-PML boundary to 3-D marine CSEM modelling by using the staggered finite-difference discretization. Numerical test indicates that the modelling algorithm using the CFS-PML also shows good accuracy compared to the Dirichlet. Furthermore, the modelling algorithm using the CFS-PML shows advantages in computational time and memory saving than that using the Dirichlet boundary. For the 3-D example in this study, the memory saving using the PML is nearly 42 per cent and the time saving is around 48 per cent compared to using the Dirichlet.

  2. Quantitative analysis of anaerobic oxidation of methane (AOM) in marine sediments: A modeling perspective

    Science.gov (United States)

    Regnier, P.; Dale, A. W.; Arndt, S.; LaRowe, D. E.; Mogollón, J.; Van Cappellen, P.

    2011-05-01

    Recent developments in the quantitative modeling of methane dynamics and anaerobic oxidation of methane (AOM) in marine sediments are critically reviewed. The first part of the review begins with a comparison of alternative kinetic models for AOM. The roles of bioenergetic limitations, intermediate compounds and biomass growth are highlighted. Next, the key transport mechanisms in multi-phase sedimentary environments affecting AOM and methane fluxes are briefly treated, while attention is also given to additional controls on methane and sulfate turnover, including organic matter mineralization, sulfur cycling and methane phase transitions. In the second part of the review, the structure, forcing functions and parameterization of published models of AOM in sediments are analyzed. The six-orders-of-magnitude range in rate constants reported for the widely used bimolecular rate law for AOM emphasizes the limited transferability of this simple kinetic model and, hence, the need for more comprehensive descriptions of the AOM reaction system. The derivation and implementation of more complete reaction models, however, are limited by the availability of observational data. In this context, we attempt to rank the relative benefits of potential experimental measurements that should help to better constrain AOM models. The last part of the review presents a compilation of reported depth-integrated AOM rates (ΣAOM). These rates reveal the extreme variability of ΣAOM in marine sediments. The model results are further used to derive quantitative relationships between ΣAOM and the magnitude of externally impressed fluid flow, as well as between ΣAOM and the depth of the sulfate-methane transition zone (SMTZ). This review contributes to an improved understanding of the global significance of the AOM process, and helps identify outstanding questions and future directions in the modeling of methane cycling and AOM in marine sediments.

  3. Microbial Impacts to the Near-Field Environment Geochemistry (MING): A Model for Estimating Microbial Communities in Repository Drifts at Yucca Mountain

    International Nuclear Information System (INIS)

    Jolley, D.M.; Ehrhorn, T.F.; Horn, J.

    2002-01-01

    Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned one million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 C and above relative humidities of 90 percent in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley and others (1997), by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift, to perform two separate mass-balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C 160 (H 280 O 80 )N 30 P 2 S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature, and pH at that time. This optimization maximizes those reactions that produce > 15kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated and unsaturated

  4. Microbial Impacts to the Near-Field Environment Geochemistry (MING): A Model for Estimating Microbial Communities in Repository Drifts at Yucca Mountain

    Energy Technology Data Exchange (ETDEWEB)

    D.M. Jolley; T.F. Ehrhorn; J. Horn

    2002-03-19

    Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned one million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 C and above relative humidities of 90 percent in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley and others (1997), by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift, to perform two separate mass-balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C{sub 160}(H{sub 280}O{sub 80})N{sub 30}P{sub 2}S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature, and pH at that time. This optimization maximizes those reactions that produce > 15kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated

  5. Development of a microbial contamination susceptibility model for private domestic groundwater sources

    Science.gov (United States)

    Hynds, Paul D.; Misstear, Bruce D.; Gill, Laurence W.

    2012-12-01

    Groundwater quality analyses were carried out on samples from 262 private sources in the Republic of Ireland during the period from April 2008 to November 2010, with microbial quality assessed by thermotolerant coliform (TTC) presence. Assessment of potential microbial contamination risk factors was undertaken at all sources, and local meteorological data were also acquired. Overall, 28.9% of wells tested positive for TTC, with risk analysis indicating that source type (i.e., borehole or hand-dug well), local bedrock type, local subsoil type, groundwater vulnerability, septic tank setback distance, and 48 h antecedent precipitation were all significantly associated with TTC presence (p source-specific design parameters were also significantly associated with bacterial presence. Hierarchical logistic regression with stepwise parameter entry was used to develop a private well susceptibility model, with the final model exhibiting a mean predictive accuracy of >80% (TTC present or absent) when compared to an independent validation data set. Model hierarchies of primary significance are source design (20%), septic tank location (11%), hydrogeological setting (10%), and antecedent 120 h precipitation (2%). Sensitivity analysis shows that the probability of contamination is highly sensitive to septic tank setback distance, with probability increasing linearly with decreases in setback distance. Likewise, contamination probability was shown to increase with increasing antecedent precipitation. Results show that while groundwater vulnerability category is a useful indicator of aquifer susceptibility to contamination, its suitability with regard to source contamination is less clear. The final model illustrates that both localized (well-specific) and generalized (aquifer-specific) contamination mechanisms are involved in contamination events, with localized bypass mechanisms dominant. The susceptibility model developed here could be employed in the appropriate location

  6. N-gram analysis of 970 microbial organisms reveals presence of biological language models

    Directory of Open Access Journals (Sweden)

    Ganapathiraju Madhavi K

    2011-01-01

    Full Text Available Abstract Background It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word usage indicative of authors or topics, and that the algorithms originally developed for natural language processing may therefore be applied to genome sequences to draw biologically relevant conclusions. Following this approach of 'biological language modeling', statistical n-gram analysis has been applied for comparative analysis of whole proteome sequences of 44 organisms. It has been shown that a few particular amino acid n-grams are found in abundance in one organism but occurring very rarely in other organisms, thereby serving as genome signatures. At that time proteomes of only 44 organisms were available, thereby limiting the generalization of this hypothesis. Today nearly 1,000 genome sequences and corresponding translated sequences are available, making it feasible to test the existence of biological language models over the evolutionary tree. Results We studied whole proteome sequences of 970 microbial organisms using n-gram frequencies and cross-perplexity employing the Biological Language Modeling Toolkit and Patternix Revelio toolkit. Genus-specific signatures were observed even in a simple unigram distribution. By taking statistical n-gram model of one organism as reference and computing cross-perplexity of all other microbial proteomes with it, cross-perplexity was found to be predictive of branch distance of the phylogenetic tree. For example, a 4-gram model from proteome of Shigellae flexneri 2a, which belongs to the Gammaproteobacteria class showed a self-perplexity of 15.34 while the cross-perplexity of other organisms was in the range of 15.59 to 29.5 and was proportional to their branching distance in the evolutionary tree from S. flexneri. The organisms of this genus, which happen to be pathotypes of E.coli, also have the closest perplexity values with

  7. Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa

    NARCIS (Netherlands)

    Rijgersberg, H.; Nierop Groot, M.N.; Tromp, S.O.; Franz, E.

    2013-01-01

    Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count

  8. Anti-Mycobacterium activity of microbial peptides in a silkworm infection model with Mycobacterium smegmatis.

    Science.gov (United States)

    Yagi, Akiho; Uchida, Ryuji; Hamamoto, Hiroshi; Sekimizu, Kazuhisa; Kimura, Ken-Ichi; Tomoda, Hiroshi

    2017-05-01

    An in vivo-mimic silkworm infection model with Mycobacterium smegmatis was established. When silkworms were raised at 37 °C following an injection of M. smegmatis cells (1.25 × 10 7 CFU larva -1  g -1 ) into the silkworm hemolymph, they died within 48 h. Under these conditions, four microbial peptides with anti-M. smegmatis activity, lariatin A, calpinactam, lysocin E and propeptin, exerted therapeutic effects in a dose-dependent manner, and these are also clinically used agents that are active against Mycobacterium tuberculosis. These results indicate that the silkworm infection model with M. smegmatis is practically useful for the screening of therapeutically effective anti-M. tuberculosis antibiotics.

  9. Stability characterization and modeling of robust distributed benthic microbial fuel cell (DBMFC) system.

    Science.gov (United States)

    Karra, Udayarka; Huang, Guoxian; Umaz, Ridvan; Tenaglier, Christopher; Wang, Lei; Li, Baikun

    2013-09-01

    A novel and robust distributed benthic microbial fuel cell (DBMFC) was developed to address the energy supply issues for oceanographic sensor network applications, especially under scouring and bioturbation by aquatic life. Multi-anode/cathode configuration was employed in the DBMFC system for enhanced robustness and stability in the harsh ocean environment. The results showed that the DBMFC system achieved peak power and current densities of 190mW/m(2) and 125mA/m(2) respectively. Stability characterization tests indicated the DBMFC with multiple anodes achieved higher power generation over the systems with single anode. A computational model that integrated physical, electrochemical and biological factors of MFCs was developed to validate the overall performance of the DBMFC system. The model simulation well corresponded with the experimental results, and confirmed the hypothesis that using a multi anode/cathode MFC configuration results in reliable and robust power generation. Published by Elsevier Ltd.

  10. A model of microbial growth in a plug flow reactor with wall attachment.

    Science.gov (United States)

    Ballyk, M; Smith, H

    1999-05-01

    A mathematical model of microbial growth for limiting nutrient in a plug flow reactor which accounts for the colonization of the reactor wall surface by the microbes is formulated and studied analytically and numerically. It can be viewed as a model of the large intestine or of the fouling of a commercial bio-reactor or pipe flow. Two steady state regimes are identified, namely, the complete washout of the microbes from the reactor and the successful colonization of both the wall and bulk fluid by the microbes. Only one steady state is stable for any particular set of parameter values. Sharp and explicit conditions are given for the stability of each, and for the long term persistence of the bacteria in the reactor.

  11. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    International Nuclear Information System (INIS)

    Jinsong Liu

    2006-04-01

    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10 5 years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10 5 years

  12. A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Dick

    Full Text Available Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as "Bison Pool" in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that

  13. A Metastable Equilibrium Model for the Relative Abundances of Microbial Phyla in a Hot Spring

    Science.gov (United States)

    Dick, Jeffrey M.; Shock, Everett L.

    2013-01-01

    Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as “Bison Pool” in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the

  14. Modeling Microbial Dynamics in Aquifers Considering the Interaction Between the Higher Trophic Levels

    Science.gov (United States)

    Bajracharya, B. M.; Cirpka, O. A.; Lu, C.

    2014-12-01

    Models of microbial dynamics coupled to solute transport in aquifers typically require the introduction of a bacterial carrying capacity term to prevent excessive microbial growth close to substrate-injection boundaries. The factors controlling this carrying capacity, however, are not fully understood. Most explanations for the occurrence of a carrying capacity discussed are based on the assumption of a bottom-up control of groundwater ecosystems. An alternative explanation is based on top-down control. Our model considers substrate, bacteria and higher trophic levels, such as grazers or bacteriophages. The dissolved substrate is transported with water flow whereas the biomasses of bacteria and grazers are considered essentially immobile. The one-dimensional reactive transport model also accounts for substrate dispersion and a random walk of grazers influenced by the bacteria concentration. The grazers grow on the bacteria, leading to a negative feedback on the bacteria concentration which may limit the turnover of the substrate. A single retentostat model with Monod kinetics of bacterial growth and a second-order grazing shows that the system oscillates but approaches a stable steady state with non-zero concentrations of substrate, bacteria, and grazers. The steady-state concentration of the bacteria biomass is independent of the substrate concentration in the inflow. When coupling several retentostats in a series to mimic a groundwater column, the steady-state bacteria concentrations remain at a constant level over a significant travel distance. The results show that grazing is a possible explanation of the carrying capacity, provided that there is enough substrate to sustain bacteria and grazers.

  15. Modeling of extracellular polymeric substances and soluble microbial products production in a submerged membrane bioreactor at various SRTs.

    Science.gov (United States)

    Ahn, Y T; Choi, Y K; Jeong, H S; Chae, S R; Shin, H S

    2006-01-01

    Extracelluar polymeric substances (EPSs) and soluble microbial products (SMPs) produced by microbial cultures involved in membrane biofouling have been widely investigated. A mathematical model of EPS and SMP formation and degradation was established based on the activated sludge model no. 1 (ASM1) and was applied to the membrane bioreactor sludge with different sludge retention times (SRTs). The unified theory that the distinct products from the EPS and SMP overlapped each other was integrated into the ASM1. Two components, five processes and eight parameters were newly added to set up the model. To increase the accuracy of model simulation, microbial kinetic parameters were determined by respirometry method and applied to the model instead of microbial kinetic constant offered in ASM1. From the respirometry result, both of heterotroph and autotroph showed different yield value, growth rate and decay rate from activated sludge. There was no significant effect of SRT on SMP production and the experimental results showed good agreement with the predicted values by the model simulation. With the developed unified EPS and SMP model, EPS and SMP production could be simulated so well that it can be applied for the membrane biofouling control.

  16. A Sense of Place: Integrating Environmental Psychology into Marine Socio-Ecological Models

    Science.gov (United States)

    van Putten, I. E.; Fleming, A.; Fulton, E.; Plaganyi-Lloyd, E.

    2016-02-01

    Sense of place is a concept that is increasingly applied in different social research contexts where it can act as a bridge between disciplines that might otherwise work in parallel. A sense of place is a well established and flexible concept that has been empirically measured using different survey methods. The psychological principals and theories that underpin sense of place have been inextricably linked to the quality of ecological systems and the impact on development of the system, and vice versa. Ecological models and scenario analyses play an important role in characterising, assessing and predicting the potential impacts of alternative developments and other changes affecting ecological systems. To improve the predictive accuracy of ecological models, human drivers, interactions, and uses have been dynamically incorporated, for instance, through management strategy evaluation applied to marine ecosystem models. However, to date no socio-ecological models (whether terrestrial or marine) have been developed that incorporate a dynamic feedback between ecosystem characteristics and peoples' sense of place. These models thus essentially ignore the influence of environmental psychology on the way people use and interact with ecosystems. We develop a proof of concept and provide a mathematical basis for a Sense of Place Index (SoPI) that allows the quantitative integration of environmental psychology into socio-ecological models. Incorporating dynamic feedback between the SoPI for different resource user groups and the ecological system improves the accuracy and precision of predictions regarding future resource use as well as, ultimately, the potential state of the resource to be developed.

  17. Rock physics modeling of shallow marine sediments in the eastern continental margin of India

    Digital Repository Service at National Institute of Oceanography (India)

    Dewangan, P.; Sriram, G.; RamPrasad, T.

    for the intermediate porosity are calculated using lower Hashin-Shtrikman bound. The fluid-saturated moduli are estimated using Gassmann’s equation. The main limitation of this model is that it requires a lot of apriori information and is computationally involved... that are in a state of suspension, i.e. having no frame stiffness. The EMM model can be extended to estimate the hydrate and free gas concentration in marine sediments from porosity and velocity profiles (Helgerud, 1999). Lee (2006) showed that shear wave...

  18. A Multianalyzer Machine Learning Model for Marine Heterogeneous Data Schema Mapping

    Directory of Open Access Journals (Sweden)

    Wang Yan

    2014-01-01

    Full Text Available The main challenges that marine heterogeneous data integration faces are the problem of accurate schema mapping between heterogeneous data sources. In order to improve the schema mapping efficiency and get more accurate learning results, this paper proposes a heterogeneous data schema mapping method basing on multianalyzer machine learning model. The multianalyzer analysis the learning results comprehensively, and a fuzzy comprehensive evaluation system is introduced for output results’ evaluation and multi factor quantitative judging. Finally, the data mapping comparison experiment on the East China Sea observing data confirms the effectiveness of the model and shows multianalyzer’s obvious improvement of mapping error rate.

  19. Mathematical model for simulation of the fate of copper in a marine environment

    International Nuclear Information System (INIS)

    Orlob, G.T.; Hrovat, D.; Wakeman, T.; Harrison, F.L.

    1979-01-01

    A mathematical model for the simulation of the fate of copper in a marine environment was developed. The model, which describes the kinetics of copper transformation from ionic copper to complexes with dissolved organic matter and sorption on suspended sediment, is imbedded in a two-dimensional finite element model which is capable of simulating advection and diffusion processes in natural receiving waters. Kinetic rate and equilibrium constants for the model were developed independently in laboratory experiments. A test simulation was performed under realistic conditions of slug discharge of ionic copper with the cooling water from a nuclear power station situated on the California coast. Results show that the model performed correctly under the conditions assumed. Future research and development is directed toward improving description of copper kinetics under varying environmental conditions and exploring the sensitivity of the model

  20. Mathematical modelling of oil spill fate and transport in the marine environment incorporating biodegradation kinetics of oil droplets

    Science.gov (United States)

    Spanoudaki, Katerina

    2016-04-01

    Oil biodegradation by native bacteria is one of the most important natural processes that can attenuate the environmental impacts of marine oil spills. However, very few numerical models of oil spill fate and transport include biodegradation kinetics of spilled oil. Furthermore, in models where biodegradation is included amongst the oil transformation processes simulated, it is mostly represented as a first order decay process neglecting the effect of several important parameters that can limit biodegradation rate, such as oil composition and oil droplets-water interface. To this end, the open source numerical model MEDSKIL-II, which simulates oil spill fate and transport in the marine environment, has been modified to include biodegradation kinetics of oil droplets dispersed in the water column. MEDSLIK-II predicts the transport and weathering of oil spills following a Lagrangian approach for the solution of the advection-diffusion equation. Transport is governed by the 3D sea currents and wave field provided by ocean circulation models. In addition to advective and diffusive displacements, the model simulates several physical and chemical processes that transform the oil (evaporation, emulsification, dispersion in the water column, adhesion to coast). The fate algorithms employed in MEDSLIK-II consider the oil as a uniform substance whose properties change as the slick weathers, an approach that can lead to reduced accuracy, especially in the estimation of oil evaporation and biodegradation. Therefore MEDSLIK-II has been modified by adopting the "pseudo-component" approach for simulating weathering processes. Spilled oil is modelled as a relatively small number of discrete, non-interacting components (pseudo-components). Chemicals in the oil mixture are grouped by physical-chemical properties and the resulting pseudo-component behaves as if it were a single substance with characteristics typical of the chemical group. The fate (evaporation, dispersion

  1. Hybrid modeling of microbial exopolysaccharide (EPS) production: The case of Enterobacter A47.

    Science.gov (United States)

    Marques, Rodolfo; von Stosch, Moritz; Portela, Rui M C; Torres, Cristiana A V; Antunes, Sílvia; Freitas, Filomena; Reis, Maria A M; Oliveira, Rui

    2017-03-20

    Enterobacter A47 is a bacterium that produces high amounts of a fucose-rich exopolysaccharide (EPS) from glycerol residue of the biodiesel industry. The fed-batch process is characterized by complex non-linear dynamics with highly viscous pseudo-plastic rheology due to the accumulation of EPS in the culture medium. In this paper, we study hybrid modeling as a methodology to increase the predictive power of models for EPS production optimization. We compare six hybrid structures that explore different levels of knowledge-based and machine-learning model components. Knowledge-based components consist of macroscopic material balances, Monod type kinetics, cardinal temperature and pH (CTP) dependency and power-law viscosity models. Unknown dependencies are set to be identified by a feedforward artificial neural network (ANN). A semiparametric identification schema is applied resorting to a data set of 13 independent fed-batch experiments. A parsimonious hybrid model was identified that describes the dynamics of the 13 experiments with the same parameterization. The final model is specific to Enterobacter A47 but can be easily extended to other microbial EPS processes. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Using habitat suitability index and particle dispersion models for early detection of marine invaders.

    Science.gov (United States)

    Inglis, Graeme J; Hurren, Helen; Oldman, John; Haskew, Rachel

    2006-08-01

    Eradication and control of invasive species are often possible only if populations are detected when they are small and localized. To be efficient, detection surveys should be targeted at locations where there is the greatest risk of incursions. We examine the utility of habitat suitability index (HSI) and particle dispersion models for targeting sampling for marine pests. Habitat suitability index models are a simple way to identify suitable habitat when species distribution data are lacking. We compared the performance of HSI models with statistical models derived from independent data from New Zealand on the distribution of two nonindigenous bivalves: Theora lubrica and Musculista senhousia. Logistic regression models developed using the HSI scores as predictors of the presence/absence of Theora and Musculista explained 26.7% and 6.2% of the deviance in the data, respectively. Odds ratios for the HSI scores were greater than unity, indicating that they were genuine predictors of the presence/ absence of each species. The fit and predictive accuracy of each logistic model were improved when simulated patterns of dispersion from the nearest port were added as a predictor variable. Nevertheless, the combined model explained, at best, 46.5% of the deviance in the distribution of Theora and correctly predicted 56% of true presences and 50% of all cases. Omission errors were between 6% and 16%. Although statistical distribution models built directly from environmental predictors always outperformed the equivalent HSI models, the gain in model fit and accuracy was modest. High residual deviance in both types of model suggests that the distributions realized by Theora and Musculista in the field data were influenced by factors not explicitly modeled as explanatory variables and by error in the environmental data used to project suitable habitat for the species. Our results highlight the difficulty of accurately predicting the distribution of invasive marine species that

  3. The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites

    Directory of Open Access Journals (Sweden)

    Gerrit Wienhausen

    2017-10-01

    Full Text Available Recent studies applying Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS showed that the exometabolome of marine bacteria is composed of a surprisingly high molecular diversity. To shed more light on how this diversity is generated we examined the exometabolome of two model strains of the Roseobacter group, Phaeobacter inhibens and Dinoroseobacter shibae, grown on glutamate, glucose, acetate or succinate by FT-ICR-MS. We detected 2,767 and 3,354 molecular formulas in the exometabolome of each strain and 67 and 84 matched genome-predicted metabolites of P. inhibens and D. shibae, respectively. The annotated compounds include late precursors of biosynthetic pathways of vitamins B1, B2, B5, B6, B7, B12, amino acids, quorum sensing-related compounds, indole acetic acid and methyl-(indole-3-yl acetic acid. Several formulas were also found in phytoplankton blooms. To shed more light on the effects of some of the precursors we supplemented two B1 prototrophic diatoms with the detected precursor of vitamin B1 HET (4-methyl-5-(β-hydroxyethylthiazole and HMP (4-amino-5-hydroxymethyl-2-methylpyrimidine and found that their growth was stimulated. Our findings indicate that both strains and other bacteria excreting a similar wealth of metabolites may function as important helpers to auxotrophic and prototrophic marine microbes by supplying growth factors and biosynthetic precursors.

  4. Modeling environmental risk factors of autism in mice induces IBD-related gut microbial dysbiosis and hyperserotonemia.

    Science.gov (United States)

    Lim, Joon Seo; Lim, Mi Young; Choi, Yongbin; Ko, GwangPyo

    2017-04-20

    Autism spectrum disorder (ASD) is a range of neurodevelopmental conditions that are sharply increasing in prevalence worldwide. Intriguingly, ASD is often accompanied by an array of systemic aberrations including (1) increased serotonin, (2) various modes of gastrointestinal disorders, and (3) inflammatory bowel disease (IBD), albeit the underlying cause for such comorbidities remains uncertain. Also, accumulating number of studies report that the gut microbial composition is significantly altered in children with ASD or patients with IBD. Surprisingly, when we analyzed the gut microbiota of poly I:C and VPA-induced mouse models of ASD, we found a distinct pattern of microbial dysbiosis that highly recapitulated those reported in clinical cases of ASD and IBD. Moreover, we report that such microbial dysbiosis led to notable perturbations in microbial metabolic pathways that are known to negatively affect the host, especially with regards to the pathogenesis of ASD and IBD. Lastly, we found that serum level of serotonin is significantly increased in both poly I:C and VPA mice, and that it correlates with increases of a bacterial genus and a metabolic pathway that are implicated in stimulation of host serotonin production. Our results using animal model identify prenatal environmental risk factors of autism as possible causative agents of IBD-related gut microbial dysbiosis in ASD, and suggest a multifaceted role of gut microbiota in the systemic pathogenesis of ASD and hyperserotonemia.

  5. Modeling of microphysics and optics of aerosol particles in the marine environments

    Science.gov (United States)

    Kaloshin, Gennady

    2013-05-01

    We present a microphysical model for the surface layer marine and coastal atmospheric aerosols that is based on long-term observations of size distributions for 0.01-100 μm particles. The fundamental feature of the model is a parameterization of amplitudes and widths for aerosol modes of the aerosol size distribution function (ASDF) as functions of fetch and wind speed. The shape of ASDF and its dependence on meteorological parameters, height above sea level (H), fetch (X), wind speed (U) and relative humidity (RH), are investigated. At present, the model covers the ranges H = 0 - 25 m, U = 3 - 18 km s-1, X ≤ 120 km and RH = 40 - 98%. The latest version of the Marine Aerosol Extinction Profiles model (MaexPro) is described and applied for the computation and analysis of the spectral profiles of aerosol extinction coefficients α(λ) in the wavelength band λ = 0.2-12 μm. MaexPro is based on the aforementioned aerosol model assuming spherically shaped aerosol particles and the well-known Mie theory. The spectral profiles of α(λ) calculated by MaexPro are in good agreement with observational data and the numerical results. Moreover, MaexPro was found to be an accurate and reliable tool for investigating the optical properties of atmospheric aerosols.

  6. Developing Theoretical Marine Habitat Suitability Models from Remotely-Sensed Data and Traditional Ecological Knowledge

    Directory of Open Access Journals (Sweden)

    Patrick M. Olsen

    2015-09-01

    Full Text Available There is a lack of information regarding critical habitats for many marine species, including the bearded seal, an important subsistence species for the indigenous residents of Arctic regions. A systematic approach to modeling marine mammal habitat in arctic regions using the lifetime and multi-generational Traditional Ecological Knowledge (TEK of Alaska Native hunters is developed to address this gap. The approach uses lifetime and cross-generational knowledge of subsistence hunters and their harvest data in the place of observational knowledge gained from Western scientific field surveys of marine mammal sightings. TEK information for mid-June to October was transformed to seal presence/pseudo-absence and used to train Classification Tree Analyses of environmental predictor variables to predict suitable habitat for bearded seals in the Bering Strait region. Predictor variables were derived from a suite of terrestrial, oceanic, and atmospheric remote sensing products, transformed using trend analysis techniques, and aggregated. A Kappa of 0.883 was achieved for habitat classifications. The TEK information used is spatially restricted, but provides a viable, replicable data source that can replace or complement Western scientific observational data.

  7. Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model.

    Science.gov (United States)

    Yasuhara, Moriaki; Tittensor, Derek P; Hillebrand, Helmut; Worm, Boris

    2017-02-01

    There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology-palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross-scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep-time perspective based on high-resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future. © 2015 Cambridge Philosophical Society.

  8. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    International Nuclear Information System (INIS)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

  9. Coupled modeling of groundwater flow solute transport, chemical reactions and microbial processes in the 'SP' island

    Energy Technology Data Exchange (ETDEWEB)

    Samper, Javier; Molinero, Jorg; Changbing, Yang; Zhang, Guoxiang

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behavior and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by /Banwart et al, 1995/. Later, /Banwart et al, 1999/ presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by /Molinero, 2000/ who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulfate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of /Molinero, 2000/ and extends the preliminary microbial model of /Zhang, 2001/ by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfate concentration, thus

  10. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    Energy Technology Data Exchange (ETDEWEB)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang [Univ. Da Coruna (Spain)

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

  11. Modeling and Control for Dynamic Positioned Marine Vessels in Drifting Managed Sea Ice

    Directory of Open Access Journals (Sweden)

    Øyvind Kåre Kjerstad

    2014-10-01

    Full Text Available This paper presents a development framework for dynamic positioning control systems for marine vessels in managed ice. Due to the complexity of the vessel-ice and ice-ice interactions a configurable high fidelity numerical model simulating the vessel, the ice floes, the water, and the boundaries is applied. The numerical model is validated using experimental data and coupled with a control application incorporating sensor models, control systems, actuator models, and other external dynamics to form a closed loop development platform. The ice drift reversal is simulated by moving the positioning reference frame in an elliptic trajectory, rather than moving each individual ice floe. A control plant model is argued, and a control system for managed ice is proposed based on conventional open water design methods. A case study shows that dynamic positioning in managed ice is feasible for some moderate ice conditions.

  12. Identifying modeled ship noise hotspots for marine mammals of Canada's Pacific region.

    Directory of Open Access Journals (Sweden)

    Christine Erbe

    Full Text Available The inshore, continental shelf waters of British Columbia (BC, Canada are busy with ship traffic. South coast waters are heavily trafficked by ships using the ports of Vancouver and Seattle. North coast waters are less busy, but expected to get busier based on proposals for container port and liquefied natural gas development and expansion. Abundance estimates and density surface maps are available for 10 commonly seen marine mammals, including northern resident killer whales, fin whales, humpback whales, and other species with at-risk status under Canadian legislation. Ship noise is the dominant anthropogenic contributor to the marine soundscape of BC, and it is chronic. Underwater noise is now being considered in habitat quality assessments in some countries and in marine spatial planning. We modeled the propagation of underwater noise from ships and weighted the received levels by species-specific audiograms. We overlaid the audiogram-weighted maps of ship audibility with animal density maps. The result is a series of so-called "hotspot" maps of ship noise for all 10 marine mammal species, based on cumulative ship noise energy and average distribution in the boreal summer. South coast waters (Juan de Fuca and Haro Straits are hotspots for all species that use the area, irrespective of their hearing sensitivity, simply due to ubiquitous ship traffic. Secondary hotspots were found on the central and north coasts (Johnstone Strait and the region around Prince Rupert. These maps can identify where anthropogenic noise is predicted to have above-average impact on species-specific habitat, and where mitigation measures may be most effective. This approach can guide effective mitigation without requiring fleet-wide modification in sites where no animals are present or where the area is used by species that are relatively insensitive to ship noise.

  13. Modeling of microbial gas generation: application to the eastern Mediterranean “Biogenic Play”

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, M.; Dubille, M.; Montadert, L.

    2016-07-01

    Biogenic gas is becoming increasingly important as an exploration target in the petroleum industry because it occurs in geologically predictable circumstances and in large quantities at shallow depths as free gas or gas hydrates. As accumulations of biogenic gas result in a subtle synchronization between early generation and early trapping, we integrated a macroscopic model of microbial gas generation within a 3D basin and petroleum system forward simulator. The macroscopic model is based on a microscopic model, which consists in a 1D sedimentary column that accounts for sedimentation, compaction, Darcy flow and Diffusion flow. The organic carbon is the only non-soluble element considered in this version of the model. The dissolved elements are O2, SO4 2-, H2, CH3COOH, and CH4. Methane is dissolved in water or present as a free phase if its concentration exceeds its solubility at given pressure and temperature. In this microscopic model, the transformation of substrate into biomass is described through a set of logistic equations coupled with the transport equations (advection and diffusion). Based on the microscopic considerations we developed the macroscopic model of low maturity/biogenic gas generation in which hydrocarbons are generated through first order kinetic reactions at low maturity. This macroscopic model is adapted to petroleum system modeling at basin scale with TemisFlow®, which aims to understand and predict hydrocarbon generation, migration, and accumulation. It is composed of: i) A source rock criteria which allow defining the biogenic gas source rocks potential and ii) A kinetic model of methane generation. The previous model has been successfully applied on different basins such as the Carupano Basin from the offshore Venezuela, the Magdalena Delta (offshore Colombia) and the offshore Vietnam where direct observations of low-maturity gas were available. Furthermore, it has been applied in the offshore Lebanon in order to check the viability of

  14. Impacts of radiation exposure on the experimental microbial ecosystem: a particle-based model simulation approach

    International Nuclear Information System (INIS)

    Doi, M.; Tanaka, N.; Fuma, S.; Kawabata, Z.

    2004-01-01

    Well-designed experimental model ecosystem could be a simple reference of the actual environment and complex ecological systems. For ecological toxicity test of radiation and other environmental toxicants, we investigated and aquatic microbial ecosystem (closed microcosm) in the test tube with initial substrates,autotroph flagellate algae (Euglena, G.), heterotroph ciliate protozoa (Tetrahymena T.) and saprotroph bacteria (E, coli). These species organizes by itself to construct the ecological system, that keeps the sustainable population dynamics for more than 2 years after inoculation only by adding light diurnally and controlling temperature at 25 degree Celsius. Objective of the study is to develop the particle-based computer simulation by reviewing interactions among microbes and environment, and analyze the ecological toxicities of radiation on the microcosm by replicating experimental results in the computer simulation. (Author) 14 refs

  15. In situ examination of microbial populations in a model drinking water distribution system

    DEFF Research Database (Denmark)

    Martiny, Adam Camillo; Nielsen, Alex Toftgaard; Arvin, Erik

    2002-01-01

    A flow cell set-up was used as a model drinking water distribution system to analyze the in situ microbial population. Biofilm growth was followed by transmission light microscopy for 81 days and showed a biofilm consisting of microcolonies separated by a monolayer of cells. Protozoans (ciliates...... revealed that the majority of the isolated strains from the bulk water and biofilm were affiliated to the family of Comamonadaceae in the β-lineage of Proteobacteria. The majority of the strains from the α-lineage were affiliated to the family of Sphingomonadaceae. We were unable to detect any strains from...... of a mixed population of α- and β-Proteobacteria. 65 strains from the inlet water and 20 from the biofilm were isolated on R2A agar plates and sorted into groups with amplified rDNA restriction analysis. The 16S rDNA gene was sequenced for representatives of the abundant groups. A phylogenetic analysis...

  16. In situ examination of microbial populations in a model drinking water distribution system

    DEFF Research Database (Denmark)

    Martiny, Adam Camillo; Nielsen, Alex Toftgaard; Arvin, Erik

    2002-01-01

    A flow cell set-up was used as a model drinking water distribution system to analyze the in situ microbial population. Biofilm growth was followed by transmission light microscopy for 81 days and showed a biofilm consisting of microcolonies separated by a monolayer of cells. Protozoans (ciliates...... of a mixed population of α- and β-Proteobacteria. 65 strains from the inlet water and 20 from the biofilm were isolated on R2A agar plates and sorted into groups with amplified rDNA restriction analysis. The 16S rDNA gene was sequenced for representatives of the abundant groups. A phylogenetic analysis...... revealed that the majority of the isolated strains from the bulk water and biofilm were affiliated to the family of Comamonadaceae in the β-lineage of Proteobacteria. The majority of the strains from the α-lineage were affiliated to the family of Sphingomonadaceae. We were unable to detect any strains from...

  17. Fine-scale habitat modeling of a top marine predator: do prey data improve predictive capacity?

    Science.gov (United States)

    Torres, Leigh G; Read, Andrew J; Halpin, Patrick

    2008-10-01

    Predators and prey assort themselves relative to each other, the availability of resources and refuges, and the temporal and spatial scale of their interaction. Predictive models of predator distributions often rely on these relationships by incorporating data on environmental variability and prey availability to determine predator habitat selection patterns. This approach to predictive modeling holds true in marine systems where observations of predators are logistically difficult, emphasizing the need for accurate models. In this paper, we ask whether including prey distribution data in fine-scale predictive models of bottlenose dolphin (Tursiops truncatus) habitat selection in Florida Bay, Florida, U.S.A., improves predictive capacity. Environmental characteristics are often used as predictor variables in habitat models of top marine predators with the assumption that they act as proxies of prey distribution. We examine the validity of this assumption by comparing the response of dolphin distribution and fish catch rates to the same environmental variables. Next, the predictive capacities of four models, with and without prey distribution data, are tested to determine whether dolphin habitat selection can be predicted without recourse to describing the distribution of their prey. The final analysis determines the accuracy of predictive maps of dolphin distribution produced by modeling areas of high fish catch based on significant environmental characteristics. We use spatial analysis and independent data sets to train and test the models. Our results indicate that, due to high habitat heterogeneity and the spatial variability of prey patches, fine-scale models of dolphin habitat selection in coastal habitats will be more successful if environmental variables are used as predictor variables of predator distributions rather than relying on prey data as explanatory variables. However, predictive modeling of prey distribution as the response variable based on

  18. Modeling Microbial Processes in EPIC to Estimate Greenhouse Gas Emissions from soils

    Science.gov (United States)

    Schwab, D. E.; Izaurralde, R. C.; McGill, W. B.; Williams, J. R.; Schmid, E.

    2009-12-01

    Emissions of trace gases (CO2, N2O and CH4) to the atmosphere from managed terrestrial ecosystems have been contributing significantly to the warming of Earth. Trace gas production is dominated by biospheric processes. An improved knowledge of the soil-plant-atmosphere interface is of key importance for understanding trace gas dynamics. In soils, microbial metabolism plays a key role in the release or uptake of trace gases. Here we present work on the biophysical and biogeochemical model EPIC (Environmental Policy/Integrated Climate) to extend its capabilities to simulate CO2 and N2O fluxes in managed and unmanaged ecosystems. Emphasis will be given to recently developed, microbially-based, denitrification and nitrification modules. The soil-atmosphere exchange of trace gases can be measured by using various equipments, but often these measurements exhibit extreme space-time variability. We use hourly time steps to account for the variability induced by small changes in environmental conditions. Soils are often studied as macroscopic systems, although their functions are predominantly controlled at a microscopic level; i.e. the level of the microorganisms. We include these processes to the extent that these are known and can be quantitatively described. We represent soil dynamics mathematically with routines for gas diffusion, Michael Menten processes, electron budgeting and other processes such as uptake and transformations. We hypothesize that maximization of energy capture form scarce substrates using energetic favorable reactions drives evolution and that competitive advantage can result by depriving a competitor from a substrate. This Microbe Model changes concepts of production of N-containing trace gases; it unifies understanding of N oxidation and reduction, predicts production and evolution of trace gases and is consistent with observations of anaerobic ammonium oxidation.

  19. The effect of corrosion inhibitors on microbial communities associated with corrosion in a model flow cell system.

    Science.gov (United States)

    Duncan, Kathleen E; Perez-Ibarra, Beatriz Monica; Jenneman, Gary; Harris, Jennifer Busch; Webb, Robert; Sublette, Kerry

    2014-01-01

    A model flow cell system was designed to investigate pitting corrosion in pipelines associated with microbial communities. A microbial inoculum producing copious amounts of H₂S was enriched from an oil pipeline biofilm sample. Reservoirs containing a nutrient solution and the microbial inoculum were pumped continuously through six flow cells containing mild steel corrosion coupons. Two cells received corrosion inhibitor "A", two received corrosion inhibitor "B", and two ("untreated") received no additional chemicals. Coupons were removed after 1 month and analyzed for corrosion profiles and biofilm microbial communities. Coupons from replicate cells showed a high degree of similarity in pitting parameters and in microbial community profiles, as determined by 16S rRNA gene sequence libraries but differed with treatment regimen, suggesting that the corrosion inhibitors differentially affected microbial species. Viable microbial biomass values were more than 10-fold higher for coupons from flow cells treated with corrosion inhibitors than for coupons from untreated flow cells. The total number of pits >10 mils diameter and maximum pitting rate were significantly correlated with each other and the total number of pits with the estimated abundance of sequences classified as Desulfomicrobium. The maximum pitting rate was significantly correlated with the sum of the estimated abundance of Desulfomicrobium plus Clostridiales, and with the sum of the estimated abundance of Desulfomicrobium plus Betaproteobacteria. The lack of significant correlation with the estimated abundance of Deltaproteobacteria suggests not all Deltaproteobacteria species contribute equally to microbiologically influenced corrosion (MIC) and that it is not sufficient to target one bacterial group when monitoring for MIC.

  20. Predictive modelling of habitat use by marine predators with respect to the abundance and depth distribution of pelagic prey

    Science.gov (United States)

    Boyd, Charlotte; Castillo, Ramiro; Hunt, George L.; Punt, André E..; VanBlaricom, Glenn R.; Weimerskirch, Henri; Bertrand, Sophie

    2015-01-01

    Understanding the ecological processes that underpin species distribution patterns is a fundamental goal in spatial ecology. However, developing predictive models of habitat use is challenging for species that forage in marine environments, as both predators and prey are often highly mobile and difficult to monitor. Consequently, few studies have dev