Relevant bibliographies by topics / Microbial metabolism

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Microbial metabolism'

Author: Grafiati
Published: 4 June 2021
Last updated: 29 July 2024

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Journal articles on the topic "Microbial metabolism"

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VINOPAL, R. T. "Microbial Metabolism." Science 239, no. 4839 (January 29, 1988): 513.2–514. http://dx.doi.org/10.1126/science.239.4839.513.

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Downs, Diana M. "Understanding Microbial Metabolism." Annual Review of Microbiology 60, no. 1 (October 2006): 533–59. http://dx.doi.org/10.1146/annurev.micro.60.080805.142308.

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ARNAUD, CELIA. "VIEWING MICROBIAL METABOLISM." Chemical & Engineering News 85, no. 38 (September 17, 2007): 11. http://dx.doi.org/10.1021/cen-v085n038.p011.

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Wackett, Lawrence P. "Microbial metabolism prediction." Environmental Microbiology Reports 2, no. 1 (February 8, 2010): 217–18. http://dx.doi.org/10.1111/j.1758-2229.2010.00144.x.

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Hahn-Hägerdal, Bärbel, and Neville Pamment. "Microbial Pentose Metabolism." Applied Biochemistry and Biotechnology 116, no. 1-3 (2004): 1207–10. http://dx.doi.org/10.1385/abab:116:1-3:1207.

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Wackett, Lawrence P. "Microbial community metabolism." Environmental Microbiology Reports 5, no. 2 (March 5, 2013): 333–34. http://dx.doi.org/10.1111/1758-2229.12041.

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Wackett, Lawrence P. "Microbial community metabolism." Environmental Microbiology Reports 15, no. 3 (May 5, 2023): 240–41. http://dx.doi.org/10.1111/1758-2229.13161.

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Rajini, K. S., P. Aparna, Ch Sasikala, and Ch V. Ramana. "Microbial metabolism of pyrazines." Critical Reviews in Microbiology 37, no. 2 (April 11, 2011): 99–112. http://dx.doi.org/10.3109/1040841x.2010.512267.

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Chubukov, Victor, Luca Gerosa, Karl Kochanowski, and Uwe Sauer. "Coordination of microbial metabolism." Nature Reviews Microbiology 12, no. 5 (March 24, 2014): 327–40. http://dx.doi.org/10.1038/nrmicro3238.

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Ash, Caroline. "Microbial entrainment of metabolism." Science 365, no. 6460 (September 26, 2019): 1414.10–1416. http://dx.doi.org/10.1126/science.365.6460.1414-j.

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Dissertations / Theses on the topic "Microbial metabolism"

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Burgess, Mary Catherine. "Insights into microbial metabolism." Thesis, Montana State University, 2012. http://etd.lib.montana.edu/etd/2012/burgess/BurgessMC0512.pdf.

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Nitrogen fixation (catalyzed by the enzyme nitrogenase), cellular respiration (completed through the Tricarboxylic Acid (TCA) cycle) and mercury detoxification (through mercury methylation) are three metabolic processes used by a wide variety of microorganisms, but that also have far reaching impacts on nutrient cycling in the environment. Roseiflexus castenholzii has been found to have a unique nitrogenase gene cluster encoding several nitrogenase homologs, including the structural proteins NifH and NifDK and the radical SAM protein, NifB, necessary for cofactor biosynthesis. However, the genome of R. castenholzii lacks the suite of nitrogenase accessory proteins necessary for nitrogen fixation. To investigate the metabolic role of these nitrogenase homologs, expression and purification protocols were developed that aid in the biochemical characterization of these proteins. Synechococcus sp. PCC 7002 encodes three novel TCA proteins, contrary to previous studies that indicated these phototrophs have incomplete TCA cycles. Expression, purification and preliminary crystallization trials were completed on the three novel TCA proteins in order to gain insight into the structure of the proteins which will elucidate the mechanism of each novel enzyme and provide evidence into the novel TCA cycle utilized by these cyanobacteria. The third project presented examines the role of microorganisms in metabolizing mercury, producing methylmercury and providing an entry point for methylmercury into the food chain in Yellowstone National Park (YNP). In this project, environmental samples were enriched for a sulfate reducing organism and a culture containing three sulfate reducing bacteria (SRB) has been established. The SRB that are present and active in the enrichment samples are known to reduce sulfate and may be responsible for the presence of methyl mercury in algal mats that bioaccumulates through the food chain in YNP. The enrichment of SRB in this culture will enable the identification and characterization of the organisms that are capable of methylating mercury in hydrothermal systems. Collectively, the results presented herein increase the knowledge base of three metabolic processes used by microorganisms: nitrogen fixation, cellular respiration through the TCA cycle and mercury detoxification; these results will contribute to a broader understanding of how these processes have evolved and their impacts on the environment.
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Patterson, Andrea Jennifer. "Microbial metabolism of organophosphonates." Thesis, University of Ulster, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.232856.

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Lister, Diane Lorraine. "The microbial metabolism of cocaine." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390042.

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Griffiths, David A. "Microbial mimicry of mammalian drug metabolism." Thesis, Cranfield University, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385132.

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Hansman, Roberta Lynn. "Microbial metabolism in the deep ocean." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3324933.

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Thesis (Ph. D.)--University of California, San Diego, 2008.
Title from first page of PDF file (viewed November 14, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Ohshiro, Takashi. "MICROBIAL SULFUR METABOLISM OF HETEROCYCLIC SULFUR COMPOUNDS." Kyoto University, 1996. http://hdl.handle.net/2433/78073.

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Chandrasekaran, Appavu. "Microbial and human metabolism of cardiac glycosides /." The Ohio State University, 1986. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487265555441466.

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Pires, Aline Mara Barbosa. "Estudos metabolicos para otimização de condições nutricionais e de cultivo para produção microbiana de acido hialuronico." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/267027.

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Orientador: Maria Helena Andrade Santana
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica
Made available in DSpace on 2018-08-14T16:51:23Z (GMT). No. of bitstreams: 1 Pires_AlineMaraBarbosa_D.pdf: 5667585 bytes, checksum: 99be814ed0f4b52809cad017f91235eb (MD5) Previous issue date: 2009
Resumo: Neste trabalho, estudou-se a otimização da produção de ácido hialurônico (HA) por cultivo de Streptococcus zooepidemicus em batelada, com base nas alterações metabólicas ao longo do cultivo. Ás condições ambientais estudadas foram a concentração inicial de glicose, controle do pH, íons minerais e fonte de nitrogênio orgânico. Nos cultivos em frascos, a concentração inicial de glicose não alterou nem o crescimento celular nem a produção de HA. Entretanto, no cultivo em biorreator sem o controle do pH, ambos foram fortemente dependentes da concentração inicial de glicose, com maior produção de HA (1,21 g.L-1) no cultivo realizado em meio com 25 g.L-1 glicose. Tal condição nutricional foi a única que apresentou maior conversão de glicose em HA (YHA/S) do que conversão de glicose em massa celular (YX/S). O controle do pH ao longo do cultivo com 25 g.L-1 glicose resultou em maior produtividade de células (0,21 g.L-1.h-1) e de HA (0,10 g.L-1.h-1). apesar dos menores rendimentos em relação à glicose. A combinação desses resultados relaciona o maior direcionamento da fonte de carbono para HA do que para células a uma resposta do microrganismo ao stress ácido ocorrido no cultivo sem controle do pH. Uma análise da distribuição dos fluxos metabólicos nas condições ambientais estudadas demonstrou que as alterações na via de produção de HA foram mais relacionadas à distribuição dos fluxos para os açúcares precursores da síntese do polímero que à disponibilidade de energia (ATP) ou potencial redutor (NADH/NAD+) das células. A total suplementação do meio de cultura com íons minerais (K+, Mg++, Na+, Fe++, Ca++, Mn++, Zn++ e Cu++) foi benéfica para o crescimento celular, porém não alterou a produção de HA de forma significativa. O estudo demonstrou ainda que a qualidade do polímero produzido pode ser modulada pela suplementação do meio com íons minerais. As propriedades reológicas do HA com baixo teor de proteína (0.44 g.g-1) e massa molar média de 4.0 x 106 Da demonstraram elevada densidade de emaranhamento das cadeias devido à alta dependência do módulo elástico com a concentração e desvios da viscosidade complexa com relação à regra de Cox-Merz. O estudo de meios alternativos contendo derivados agroindustriais demonstrou maiores concentrações de HA em meios contendo extrato de levedura como fonte de nitrogênio. Este conjunto de resultados contribui para a otimização da produção de HA, assim como para um melhor entendimento do metabolismo do Streptococcus zooepidemicus.
Abstract: In this work, h was studied the optimization of HA production by hatch culture of Streptococcus zooepidemicus, with focus on the metabolic changes along cultivation. The environmental conditions studied were the initial glucose concentration, pH control, mineral ions and organic nitrogen source. In flask cultivations, the initial glucose concentration had no influence on the amounts of either the biomass or the MA produced. However, in bioreactor cultivations, at non-controlled pH. both were strongly dependent on the initial glucose concentration. The highest HA concentration (1.21 g.L-1) was obtained from 25 g.L-1 glucose, which was the only cultivation where the conversion of glucose to HA (YHA/S) was higher than the one of glucose to biomass (YX/S). Not only did the pH control along cultivation result in higher cell productivity (0.21 g.L-1.h-1), but also in the HA productivity (0.10 g.L-1.h-1), However, the HA and cell yields from glucose were lower. The combination of these results relates the higher direction of the carbon source to the HA synthesis at the expenses of the cell growth to a microbial response to the acid stress observed in non-controlled pH. An analysis of the metabolic flux distribution in the environmental conditions studied shows that the changes in the HA production pathway were more related to die distributions of duxes 10 the precursors of HA synthesis than to the energy availability (ATP) or redox slate (NADH/NAD+) of the cells. The total supplementation of the culture medium with ions was beneficial to die cell growth. However, if did not have any influence on the HA production. Moreover, the results showed that the HA quality may be modulated through the mineral ion supplementation. The rheological properties of HA with low protein content (0.44 g.g-1) and average molecular weight of 4.0 x 106 Da showed the high entanglements density of the HA chains due to the high storage modulus concentration dependence as well as to the complex viscosity deviations with respect to the Cox - Merz rule. Alternative media containing agricultural resources derivates were studied. The higher HA concentrations were produced in media whose organic nitrogen source was yeast extract. This set of results contributes not only to the optimization of the HA production, but also to a better understanding of the Streptococcus zooepidemicus metabolism.
Doutorado
Desenvolvimento de Processos Biotecnologicos
Doutor em Engenharia Química
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Johnson, Winifred M. Ph D. Massachusetts Institute of Technology. "Linking microbial metabolism and organic matter cycling through metabolite distributions in the ocean." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/108909.

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Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Key players in the marine carbon cycle are the ocean-dwelling microbes that fix, remineralize, and transform organic matter. Many of the small organic molecules in the marine carbon pool have not been well characterized and their roles in microbial physiology, ecological interactions, and carbon cycling remain largely unknown. In this dissertation metabolomics techniques were developed and used to profile and quantify a suite of metabolites in the field and in laboratory experiments. Experiments were run to study the way a specific metabolite can influence microbial metabolite output and potentially processing of organic matter. Specifically, the metabolic response of the heterotrophic marine bacterium, Ruegeria pomeroyi, to the algal metabolite dimethylsulfoniopropionate (DMSP) was analyzed using targeted and untargeted metabolomics. The manner in which DMSP causes R. pomeroyi to modify its biochemical pathways suggests anticipation by R. pomeroyi of phytoplankton-derived nutrients and higher microbial density. Targeted metabolomics was used to characterize the latitudinal and vertical distributions of particulate and dissolved metabolites in samples gathered along a transect in the Western Atlantic Ocean. The assembled dataset indicates that, while many metabolite distributions co-vary with biomass abundance, other metabolites show distributions that suggest abiotic, species specific, or metabolic controls on their variability. On sinking particles in the South Atlantic portion of the transect, metabolites possibly derived from degradation of organic matter increase and phytoplankton-derived metabolites decrease. This work highlights the role DMSP plays in the metabolic response of a bacterium to the environment and reveals unexpected ways metabolite abundances vary between ocean regions and are transformed on sinking particles. Further metabolomics studies of the global distributions and interactions of marine biomolecules promise to provide new insights into microbial processes and metabolite cycling.
by Winifred M. Johnson.
Ph. D.
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Newbold, Charles James. "Microbial metabolism of lactic acid in the rumen." Thesis, University of Glasgow, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235529.

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Books on the topic "Microbial metabolism"

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Dahl, Christiane, and Cornelius G. Friedrich, eds. Microbial Sulfur Metabolism. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72682-1.

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Christiane, Dahl, and Friedrich Cornelius G, eds. Microbial sulfur metabolism. Berlin: Springer, 2008.

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Spormann, Alfred M. Principles of Microbial Metabolism and Metabolic Ecology. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-28218-8.

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Caldwell, Daniel R. Microbial physiology and metabolism. 2nd ed. Belmont, Calif: Star, 1999.

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Patterson, Andrea Jennifer. Microbial metabolism of organophosphonates. [S.l: The Author], 2001.

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K, Poole Robert, Dow Crawford S, and Society for General Microbiology. Cell Biology Group., eds. Microbial gas metabolism: Mechanistic, metabolic, and biotechnological aspects. London: Published for the Society for General Microbiology by Academic Press, 1985.

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Stolz, John F., and Ronald S. Oremland, eds. Microbial Metal and Metalloid Metabolism. Washington, DC, USA: ASM Press, 2011. http://dx.doi.org/10.1128/9781555817190.

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Winkelmann, Günther, and Carl J. Carrano. Transition Metals in Microbial Metabolism. London: CRC Press, 2022. http://dx.doi.org/10.1201/9781003211129.

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Arora, Pankaj Kumar, ed. Microbial Metabolism of Xenobiotic Compounds. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-7462-3.

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Günther, Winkelmann, and Carrano Carl J, eds. Transition metals in microbial metabolism. Amsterdam: Harwood Academic Publishers, 1997.

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Book chapters on the topic "Microbial metabolism"

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Spormann, Alfred M. "Microbial Energetics." In Principles of Microbial Metabolism and Metabolic Ecology, 35–57. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-28218-8_3.

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Spormann, Alfred M. "Microbial Kinetics." In Principles of Microbial Metabolism and Metabolic Ecology, 73–97. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-28218-8_5.

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Hahn-Hägerdal, Bärbel, and Neville Pamment. "Microbial Pentose Metabolism." In Proceedings of the Twenty-Fifth Symposium on Biotechnology for Fuels and Chemicals Held May 4–7, 2003, in Breckenridge, CO, 1207–9. Totowa, NJ: Humana Press, 2004. http://dx.doi.org/10.1007/978-1-59259-837-3_97.

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Hausinger, Robert P. "Microbial Nickel Metabolism." In Biochemistry of Nickel, 181–201. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4757-9435-9_7.

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Tiquia-Arashiro, Sonia M. "Microbial CO Metabolism." In Thermophilic Carboxydotrophs and their Applications in Biotechnology, 5–9. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11873-4_2.

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Wall, Judy D., Adam P. Arkin, Nurgul C. Balci, and Barbara Rapp-Giles. "Genetics and Genomics of Sulfate Respiration in Desulfovibrio." In Microbial Sulfur Metabolism, 1–12. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72682-1_1.

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Chan, Leong-Keat, Rachael Morgan-Kiss, and Thomas E. Hanson. "Sulfur Oxidation in Chlorobium tepidum (syn. Chlorobaculum tepidum): Genetic and Proteomic Analyses." In Microbial Sulfur Metabolism, 117–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72682-1_10.

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Stout, Jan, Lina De Smet, Bjorn Vergauwen, Savvas Savvides, and Jozef Van Beeumen. "Structural Insights into Component SoxY of the Thiosulfate-Oxidizing Multienzyme System of Chlorobaculum thiosulfatiphilum." In Microbial Sulfur Metabolism, 127–38. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72682-1_11.

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Friedrich, Cornelius G., Armin Quentmeier, Frank Bardischewsky, Dagmar Rother, Grazyna Orawski, Petra Hellwig, and Jürg Fischer. "Redox Control of Chemotrophic Sulfur Oxidation of Paracoccus pantotrophus." In Microbial Sulfur Metabolism, 139–50. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72682-1_12.

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Kappler, Ulrike. "Bacterial Sulfite-Oxidizing Enzymes – Enzymes for Chemolithotrophs Only?" In Microbial Sulfur Metabolism, 151–69. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72682-1_13.

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Conference papers on the topic "Microbial metabolism"

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Khanna, Namrata, Tanushri Chatterji, Suruchi Singh, and Poonam Chaturvedi. "Microbial metabolism in bioremediation: A review." In THE FOURTH SCIENTIFIC CONFERENCE FOR ELECTRICAL ENGINEERING TECHNIQUES RESEARCH (EETR2022). AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0163146.

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Poulain, Alexandre, Daniel Gregoire, Noemie Lavoie, and Benjamin Stenzler. "Mitigating Hg Pollution by Harnessing Anaerobic Microbial Metabolism." In Goldschmidt2020. Geochemical Society, 2020. http://dx.doi.org/10.46427/gold2020.2110.

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Brodie, E., P. Sorensen, U. Karaoz, D. Chadwick, N. Falco, N. Bouskill, H. Wainwright, et al. "Remote Sensing of Microbial Metabolism from Genomes to Ecosystems." In NSG2021 27th European Meeting of Environmental and Engineering Geophysics. European Association of Geoscientists & Engineers, 2021. http://dx.doi.org/10.3997/2214-4609.202120225.

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Ryan-Baker, M., Tuan Vo-Dinh, Guy D. Griffin, Gordon H. Miller, Jean P. Alarie, Robert S. Burlage, A. V. Palumbo, Dennis C. White, and S. Herbes. "Optical monitor for microbial metabolism for hazardous waste application." In OE/LASE '92, edited by Tuan Vo-Dinh. SPIE, 1992. http://dx.doi.org/10.1117/12.59339.

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Luo, Tianqi, Daniel R. Bond, and Joseph J. Talghader. "Photoresponse of Diode-Biased Microelectrodes for Enhanced Microbial Metabolism." In 2023 International Conference on Optical MEMS and Nanophotonics (OMN) and SBFoton International Optics and Photonics Conference (SBFoton IOPC). IEEE, 2023. http://dx.doi.org/10.1109/omn/sbfotoniopc58971.2023.10230982.

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Gaskins, H. Rex. "Abstract SS01-02: Microbial sulfur metabolism and colorectal cancer risk." In Abstracts: Sixth AACR Conference: The Science of Cancer Health Disparities; December 6–9, 2013; Atlanta, GA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7755.disp13-ss01-02.

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Siddique, Tariq, and Julia Foght. "Methane Emissions from Oil Sand Tailings by Microbial Metabolism of Hydrocarbons." In Environmental Management and Engineering / Unconventional Oil. Calgary,AB,Canada: ACTAPRESS, 2011. http://dx.doi.org/10.2316/p.2011.731-027.

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Hubert, C., M. Nemati, G. Voordouw, and G. E. Jenneman. "Biogenic Sulfide Production in Continuous Systems: Containment Strategies Targeting Microbial Metabolism." In Canadian International Petroleum Conference. Petroleum Society of Canada, 2002. http://dx.doi.org/10.2118/2002-114-ea.

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Gohier, C., and L. Drouet. "Reducing crude protein in diet by stimulating ruminal microbial growth with essential oils." In 6th EAAP International Symposium on Energy and Protein Metabolism and Nutrition. The Netherlands: Wageningen Academic Publishers, 2019. http://dx.doi.org/10.3920/978-90-8686-891-9_42.

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Udegbunam, E. O., J. P. Adkins, R. M. Knapp, M. J. McInerney, and R. S. Tanner. "Assessing the Effects of Microbial Metabolism and Metabolites on Reservoir Pore Structure." In SPE Annual Technical Conference and Exhibition. Society of Petroleum Engineers, 1991. http://dx.doi.org/10.2118/22846-ms.

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Reports on the topic "Microbial metabolism"

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McKinlay, James B. Metabolism and Evolution of a Biofuel-Producing Microbial Coculture. Office of Scientific and Technical Information (OSTI), June 2018. http://dx.doi.org/10.2172/1459596.

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Lovley, Derek R. Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques. Office of Scientific and Technical Information (OSTI), November 2012. http://dx.doi.org/10.2172/1097098.

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Lovley, Derek R. Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques. Office of Scientific and Technical Information (OSTI), November 2012. http://dx.doi.org/10.2172/1055767.

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Sarvaiya, Niral, and Vijay Kothari. Audible sound in form of music can influence microbial growth, metabolism, and antibiotic susceptibility. Cold Spring Harbor Laboratory, March 2016. http://dx.doi.org/10.1101/044776.

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Konisky, J. International Symposium on Topics in Microbial Diversity, Metabolism, and Physiology. Final report, May 22--23, 1992. Office of Scientific and Technical Information (OSTI), July 1993. http://dx.doi.org/10.2172/10158099.

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Hofmockel, Kirsten. Microbial drivers of global change at the aggregate scale: linking genomic function to carbon metabolism and warming. Office of Scientific and Technical Information (OSTI), June 2019. http://dx.doi.org/10.2172/1524429.

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Droby, S., J. L. Norelli, M. E. Wisniewski, S. Freilich, A. Faigenboim, and C. Dardick. Microbial networks on harvested apples and the design of antagonistic consortia to control postharvest pathogens. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134164.bard.

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We have demonstrated, at a global level, the existence of spatial variation in the fungal and bacterial composition of different fruit tissues. The composition, diversity and abundance varied in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was determined and found to be represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. To further characterize apple fruit the microbiome after harvest, a detailed study was performed to evaluate effects of postharvest practices on the composition of the fruit peel. Microbiota. Results of this work conformed our findings that tissue-type is the main factor driving fungal and bacterial diversity and community composition on apple fruit. Both postharvest treatments and low temperature storage had a great impact on the fungal and bacterial diversity and community composition of these tissue types. Distinct spatial and temporal changes in the composition and diversity of the microbiota were observed in response to various postharvest management practices. Our results clearly indicated that apple fruit has a unique core microbiome that is universal. Analysis of the microbiome across Malus species indicates that the microbiome of domesticated apple has a higher diversity and abundance and is an admixture of the microbiome present in its wild progenitors, with clear evidence for introgression. These findings support the existence of co-evolution between Malus species and their microbiome during domestication. A network analysis of the metagenomics data was used to further elucidate functional differences between the microbiome of organic vs. conventional fruit. Our analysis predicted a link between Capnodiales and the degradation of aromatic compounds. Alternaria, a genus in the Capnodiales genus, is one of the main pathogens of stored apple fruit and was also abundant in our samples. The potential role of Alternaria in the degradation of aromatic compounds is in agreement with previous studies indicating a link between Alternaria and the metabolism of the aromatic compound, alphafarnesene38, a key volatile secreted by the fruit during maturation. A greater number of metabolic pathways related to plant defense substances (e.g. terpenoids and alkaloids) were identified in the microbiome of organic fruit samples, while more antibiotic-related metabolic pathways for compounds such as Erythromycin, Avermectin, Ansamycin, and Penicillin were present in the microbiome of apple fruit samples grown using conventional management practices.
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8

Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.

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Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report
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9

TURICK, CHARLES. Microbial Metabolite Production for Accelerated Metal and Radionuclide Bioremediation (Microbial Metabolite Production Report). Office of Scientific and Technical Information (OSTI), September 2004. http://dx.doi.org/10.2172/835058.

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10

Varga, Gabriella A., Amichai Arieli, Lawrence D. Muller, Haim Tagari, Israel Bruckental, and Yair Aharoni. Effect of Rumen Available Protein, Amimo Acids and Carbohydrates on Microbial Protein Synthesis, Amino Acid Flow and Performance of High Yielding Cows. United States Department of Agriculture, August 1993. http://dx.doi.org/10.32747/1993.7568103.bard.

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The effect of rumen available protein amino acids and carbohydrates on microbial protein synthesis, amino acid flow and performance of high yielding dairy cows was studied. A significant relationship between the effective degradabilities of OM in feedstuffs and the in vivo ruminal OM degradation of diets of dairy cows was found. The in situ method enabled the prediction of ruminal nutrients degradability response to processing of energy and nitragenous supplements. The AA profile of the rumen undegradable protein was modified by the processing method. In a continuous culture study total N and postruminal AA flows, and bacterial efficiency, is maximal at rumen degradable levels of 65% of the CP. Responses to rumen degradable non carbohydrate (NSC) were linear up to at least 27% of DM. Higher CP flow in the abomasum was found for cows fed high ruminally degradable OM and low ruminally degradable CP diet. It appeared that in dairy cows diets, the ratio of rumen degradable OM to rumenally degradable CP should be at least 5:1 in order to maximize postruminal CP flow. The efficiency of microbial CP synthesis was higher for diets supplemented with 33% of rumen undegradable protein, with greater amounts of bacterial AA reaching the abomasum. Increase in ruminal carbohydrate availability by using high moisture corn increased proportions of propionate, postruminal nutrients flow, postruminal starch digestibility, ruminal availability of NSC, uptake of energy substrates by the mammory gland. These modifications resulted with improvement in the utilization of nonessential AA for milk protein synthesis, in higher milk protein yield. Higher postruminal NSC digestibility and higher efficiency of milk protein production were recorded in cows fed extruded corn. Increasing feeding frequency increased flow of N from the rumen to the blood, reduced diurnal variation in ruminal and ammonia, and of plasma urea and improved postruminal NSC and CIP digestibility and total tract digestibilities. Milk and constituent yield increased with more frequent feeding. In a study performed in a commercial dairy herd, changes in energy and nitrogenous substrates level suggested that increasing feeding frequency may improve dietary nitrogen utilization and may shift metabolism toward more glucogenesis. It was concluded that efficiency of milk protein yield in high producing cows might be improved by an optimization of ruminal and post-ruminal supplies of energy and nitrogenous substrates. Such an optimization can be achieved by processing of energy and nitrogenous feedstuffs, and by increasing feeding frequency. In situ data may provide means for elucidation of the optimal processing conditions.
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