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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Geologic Sediments

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Disease relevance of Geologic Sediments


High impact information on Geologic Sediments

  • A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments [6].
  • Here we report the first recognition of 2,6,10,15,19-pentamethyleicosane (II), a known component of methanogens, in marine sediments of Recent to Cretaceous age (Table 1) and suggest that it and certain other acyclic isoprenoids may be used as biological markers for methanogens [7].
  • Laboratory experiments with DDE-containing marine sediments showed that DDE is dechlorinated to DDMU in both methanogenic and sulfidogenic microcosms and that DDD is dehydrochlorinated to DDMU three orders of magnitude more slowly [8].
  • The SPME-GC-MIP-AES method was validated using several marine sediment and tissue matrix certified reference materials (CRMs) with certified values for methylmercury and butyltin compounds [9].
  • A method is described for the determination of methylmercury and butyltin compounds in marine sediment and tissue using microwave-assisted acid extraction or digestion and solid-phase microextraction (SPME) followed by analysis using gas chromatography with microwave-induced plasma atomic emission spectrometric detection (GC-MIP-AES) [9].

Chemical compound and disease context of Geologic Sediments


Biological context of Geologic Sediments


Associations of Geologic Sediments with chemical compounds

  • Reductive dechlorination of DDE to DDMU in marine sediment microcosms [8].
  • At a pH near 8, where >95% of total sulfide is present as HS-, the results are indistinguishable from total sulfide measured using the methylene blue method in a wide range of sample types and matrixes including freshwater from groundwater wells, marine hydrothermal vent fluids, and marine sediment porewaters [16].
  • Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments [17].
  • Incubation of marine sediment in anoxic, sulphate-rich medium in the presence of naphthalene resulted in the enrichment of sulphate-reducing bacteria [18].
  • Production of N(2) through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments [19].

Gene context of Geologic Sediments

  • Three unique marine sediment nosZ genes were identified and sequenced [20].
  • An actinobacterial strain was isolated from marine sediment taken from the Troitsa Bay of the Gulf of Peter the Great, East Siberian Sea, and subjected to a taxonomic investigation [21].
  • Forty-five marine sediments from the Catalonian coast were analyzed for non-ortho and mono-ortho chlorine substituted PCB congeners, PCDDs and PCDFs, and 16 PAHs [22].
  • The application of this analytical procedure has allowed one to determined PAH isotopic composition in a reference material crude oil (SRM 1582) and a marine sediment (SRM 1944) with good reproducibility as uncertainties between three independent assays performed were lower than 0.5 per thousand [23].
  • In the present study, a novel obligately respiratory, denitrifying and RDX-mineralizing bacterium, designated strain HAW-EB4(T), was isolated from the marine sediment [24].

Analytical, diagnostic and therapeutic context of Geologic Sediments

  • To characterize the growth and physiology of these anaerobic methanotrophs and the syntrophic sulfate-reducing bacteria, we incubated marine sediments using an anoxic, continuous-flow bioreactor during two experiments at different advective porewater flow rates [25].
  • A supercritical fluid extraction (SFE) procedure for Irgarol 1051 (i.e. 2-(tert-butylamino)-4-(cyclopropylamino)-6-(methylthio)-1,3,5-triazine) determination in marine sediments, which minimises the solvent usage, is developed and compared to a conventional extraction technique (i.e. sonication) [26].


  1. Distribution of tetracycline resistance determinants among gram-negative bacteria isolated from polluted and unpolluted marine sediments. Andersen, S.R., Sandaa, R.A. Appl. Environ. Microbiol. (1994) [Pubmed]
  2. Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments. Mussmann, M., Schulz, H.N., Strotmann, B., Kjaer, T., Nielsen, L.P., Rosselló-Mora, R.A., Amann, R.I., Jørgensen, B.B. Environ. Microbiol. (2003) [Pubmed]
  3. Evidence that Escherichia coli accumulates glycine betaine from marine sediments. Ghoul, M., Bernard, T., Cormier, M. Appl. Environ. Microbiol. (1990) [Pubmed]
  4. Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment. Zhao, J.S., Manno, D., Beaulieu, C., Paquet, L., Hawari, J. Int. J. Syst. Evol. Microbiol. (2005) [Pubmed]
  5. Toxicity of 1,4-dichlorobenzene in sediments to juvenile polychaete worms. McPherson, C.A., Tang, A., Chapman, P.M., Taylor, L.A., Gormican, S.J. Mar. Pollut. Bull. (2002) [Pubmed]
  6. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jørgensen, B.B., Witte, U., Pfannkuche, O. Nature (2000) [Pubmed]
  7. Specific acyclic isoprenoids as biological markers of methanogenic bacteria in marine sediments. Brassell, S.C., Wardroper, A.M., Thomson, I.D., Maxwell, J.R., Eglinton, G. Nature (1981) [Pubmed]
  8. Reductive dechlorination of DDE to DDMU in marine sediment microcosms. Quensen, J.F., Mueller, S.A., Jain, M.K., Tiedje, J.M. Science (1998) [Pubmed]
  9. Determination of methylmercury and butyltin compounds in marine biota and sediments using microwave-assisted acid extraction, solid-phase microextraction, and gas chromatography with microwave-induced plasma atomic emission spectrometric detection. Tutschku, S., Schantz, M.M., Wise, S.A. Anal. Chem. (2002) [Pubmed]
  10. Importance of Gram-positive naphthalene-degrading bacteria in oil-contaminated tropical marine sediments. Zhuang, W.Q., Tay, J.H., Maszenan, A.M., Krumholz, L.R., Tay, S.T. Lett. Appl. Microbiol. (2003) [Pubmed]
  11. Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling. Urakawa, H., Yoshida, T., Nishimura, M., Ohwada, K. Environ. Microbiol. (2000) [Pubmed]
  12. Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Morris, R.M., Rappé, M.S., Urbach, E., Connon, S.A., Giovannoni, S.J. Appl. Environ. Microbiol. (2004) [Pubmed]
  13. Isolation of broad-host-range replicons from marine sediment bacteria. Sobecky, P.A., Mincer, T.J., Chang, M.C., Toukdarian, A., Helinski, D.R. Appl. Environ. Microbiol. (1998) [Pubmed]
  14. A quantitative relationship that demonstrates mercury methylation rates in marine sediments are based on the community composition and activity of sulfate-reducing bacteria. King, J.K., Kostka, J.E., Frischer, M.E., Saunders, F.M., Jahnke, R.A. Environ. Sci. Technol. (2001) [Pubmed]
  15. Sorption-desorption behaviour of 2,4-dichlorophenol by marine sediments. Fytianos, K., Voudrias, E., Kokkalis, E. Chemosphere (2000) [Pubmed]
  16. Direct ultraviolet spectrophotometric determination of total sulfide and iodide in natural waters. Guenther, E.A., Johnson, K.S., Coale, K.H. Anal. Chem. (2001) [Pubmed]
  17. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Orphan, V.J., Hinrichs, K.U., Ussler, W., Paull, C.K., Taylor, L.T., Sylva, S.P., Hayes, J.M., Delong, E.F. Appl. Environ. Microbiol. (2001) [Pubmed]
  18. Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium. Galushko, A., Minz, D., Schink, B., Widdel, F. Environ. Microbiol. (1999) [Pubmed]
  19. Production of N(2) through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Thamdrup, B., Dalsgaard, T. Appl. Environ. Microbiol. (2002) [Pubmed]
  20. Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. Scala, D.J., Kerkhof, L.J. FEMS Microbiol. Lett. (1998) [Pubmed]
  21. Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment. Kim, S.B., Nedashkovskaya, O.I., Mikhailov, V.V., Han, S.K., Kim, K.O., Rhee, M.S., Bae, K.S. Int. J. Syst. Evol. Microbiol. (2004) [Pubmed]
  22. Toxic potency assessment of non- and mono-ortho PCBs, PCDDs, PCDFs, and PAHs in northwest Mediterranean sediments (Catalonia, Spain). Eljarrat, E., Caixach, J., Rivera, J., de Torres, M., Ginebreda, A. Environ. Sci. Technol. (2001) [Pubmed]
  23. Polycyclic aromatic hydrocarbon 13C/12C ratio measurement in petroleum and marine sediments application to standard reference materials and a sediment suspected of contamination from the Erika oil spill. Mazeas, L., Budzinski, H. Journal of chromatography. A. (2001) [Pubmed]
  24. Shewanella halifaxensis sp. nov., a novel obligately respiratory and denitrifying psychrophile. Zhao, J.S., Manno, D., Leggiadro, C., O'Neil, D., Hawari, J. Int. J. Syst. Evol. Microbiol. (2006) [Pubmed]
  25. Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor. Girguis, P.R., Cozen, A.E., DeLong, E.F. Appl. Environ. Microbiol. (2005) [Pubmed]
  26. Determination of Irgarol 1051 in Western Mediterranean sediments. Development and application of supercritical fluid extraction-immunoaffinity chromatography procedure. Carrasco, P.B., Díez, S., Jiménez, J., Marco, M.P., Bayona, J.M. Water Res. (2003) [Pubmed]
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