geologic sediments

Summary

Summary: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)

Top Publications

  1. pmc Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
    Christopher A Francis
    Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:14683-8. 2005
  2. pmc Global distribution of microbial abundance and biomass in subseafloor sediment
    Jens Kallmeyer
    Institut für Erd und Umweltwissenschaften, Universitat Potsdam, 14476 Potsdam, Germany
    Proc Natl Acad Sci U S A 109:16213-6. 2012
  3. pmc Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment
    Jennifer F Biddle
    Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 105:10583-8. 2008
  4. ncbi Geographic barriers isolate endemic populations of hyperthermophilic archaea
    Rachel J Whitaker
    Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
    Science 301:976-8. 2003
  5. ncbi Significant contribution of Archaea to extant biomass in marine subsurface sediments
    Julius S Lipp
    Organic Geochemistry Group, Department of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, 28334 Bremen, Germany
    Nature 454:991-4. 2008
  6. ncbi A marine microbial consortium apparently mediating anaerobic oxidation of methane
    A Boetius
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Nature 407:623-6. 2000
  7. ncbi Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment
    Bente Aa Lomstein
    Department of Bioscience, Section for Microbiology, Aarhus University, Building 1540, Ny Munkegade 114, DK 8000 Aarhus C, Denmark
    Nature 484:101-4. 2012
  8. pmc The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments
    Christina Bienhold
    HGF MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
    ISME J 6:724-32. 2012
  9. ncbi A taxa-area relationship for bacteria
    M Claire Horner-Devine
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Nature 432:750-3. 2004
  10. pmc Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru
    Jennifer F Biddle
    Pennsylvania State Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 103:3846-51. 2006

Detail Information

Publications335 found, 100 shown here

  1. pmc Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
    Christopher A Francis
    Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:14683-8. 2005
    ..Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle...
  2. pmc Global distribution of microbial abundance and biomass in subseafloor sediment
    Jens Kallmeyer
    Institut für Erd und Umweltwissenschaften, Universitat Potsdam, 14476 Potsdam, Germany
    Proc Natl Acad Sci U S A 109:16213-6. 2012
    ..In consequence, we estimate Earth's total number of microbes and total living biomass to be, respectively, 50-78% and 10-45% lower than previous estimates...
  3. pmc Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment
    Jennifer F Biddle
    Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 105:10583-8. 2008
    ..These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups...
  4. ncbi Geographic barriers isolate endemic populations of hyperthermophilic archaea
    Rachel J Whitaker
    Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
    Science 301:976-8. 2003
    ..The identification of a biogeographic pattern in the archaeon Sulfolobus challenges the current model of microbial biodiversity in which unrestricted dispersal constrains the development of global species richness...
  5. ncbi Significant contribution of Archaea to extant biomass in marine subsurface sediments
    Julius S Lipp
    Organic Geochemistry Group, Department of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, 28334 Bremen, Germany
    Nature 454:991-4. 2008
    ..Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets...
  6. ncbi A marine microbial consortium apparently mediating anaerobic oxidation of methane
    A Boetius
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Nature 407:623-6. 2000
    ..These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane...
  7. ncbi Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment
    Bente Aa Lomstein
    Department of Bioscience, Section for Microbiology, Aarhus University, Building 1540, Ny Munkegade 114, DK 8000 Aarhus C, Denmark
    Nature 484:101-4. 2012
    ....
  8. pmc The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments
    Christina Bienhold
    HGF MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
    ISME J 6:724-32. 2012
    ....
  9. ncbi A taxa-area relationship for bacteria
    M Claire Horner-Devine
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Nature 432:750-3. 2004
    ..This relationship was driven primarily by environmental heterogeneity rather than geographic distance or plant composition...
  10. pmc Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru
    Jennifer F Biddle
    Pennsylvania State Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 103:3846-51. 2006
    ..Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea...
  11. ncbi Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments
    Bonnie Laverock
    Plymouth Marine Laboratory, Plymouth, UK
    ISME J 4:1531-44. 2010
    ..In an area of high macrofaunal abundance, this could lead to alterations in the microbial transformations of important nutrients at the sediment-water interface...
  12. ncbi Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments
    Emily B Hollister
    Department of Soil and Crop Sciences, Texas A and M University, College Station, TX 77843 2474, USA
    ISME J 4:829-38. 2010
    ..The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems...
  13. ncbi Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary
    Annika C Mosier
    Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA
    Environ Microbiol 10:3002-16. 2008
    ..Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive...
  14. ncbi Microbial population structures in the deep marine biosphere
    Julie A Huber
    Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
    Science 318:97-100. 2007
    ....
  15. ncbi Uncultured archaea in deep marine subsurface sediments: have we caught them all?
    Andreas Teske
    Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    ISME J 2:3-18. 2008
    ....
  16. ncbi Feast and famine--microbial life in the deep-sea bed
    Bo Barker Jørgensen
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D 28359, Germany
    Nat Rev Microbiol 5:770-81. 2007
    ..Here, we review microbial biodiversity and function in these intriguing environments...
  17. pmc Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara
    Achim Quaiser
    Unité d Ecologie, Systematique et Evolution, CNRS UMR8079, Universite Paris Sud 11, Orsay, France
    ISME J 5:285-304. 2011
    ..The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles...
  18. ncbi Reverse methanogenesis: testing the hypothesis with environmental genomics
    Steven J Hallam
    Monterey Bay Aquarium Research Institute, Moss Landing, CA 95064, USA
    Science 305:1457-62. 2004
    ..These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation...
  19. ncbi Environmental impacts of dredging and other sediment disturbances on corals: a review
    Paul L A Erftemeijer
    Sinclair Knight Merz SKM, P O Box H615, Perth, WA 6001, Australia
    Mar Pollut Bull 64:1737-65. 2012
    ....
  20. ncbi Oxygen and the spatial structure of microbial communities
    Tom Fenchel
    Marine Biological Laboratory, University of Copenhagen, Strandpromenaden 5, DK 3000 Helsingør, Denmark
    Biol Rev Camb Philos Soc 83:553-69. 2008
    ..Thus the oxygenated sediments surrounding ventilated animal burrows provide a special habitat for metazoan meiofauna as well as unicellular organisms...
  21. ncbi Coral record of increased sediment flux to the inner Great Barrier Reef since European settlement
    Malcolm McCulloch
    Research School of Earth Sciences, Australian National University, Canberra 0200, Australia
    Nature 421:727-30. 2003
    ....
  22. ncbi Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean
    Regina Schauer
    Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    ISME J 4:159-70. 2010
    ....
  23. pmc Production of N(2) through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments
    Bo Thamdrup
    Danish Center for Earth System Science, Institute of Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Appl Environ Microbiol 68:1312-8. 2002
    ..The process can explain ammonium deficiencies in anoxic waters and sediments, and it may contribute significantly to oceanic nitrogen budgets...
  24. ncbi Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico
    Robert J Martinez
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Environ Microbiol 8:1783-96. 2006
    ..This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano...
  25. ncbi Abundance and diversity of microbial life in ocean crust
    Cara M Santelli
    MIT WHOI Joint Program in Oceanography and Ocean Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA
    Nature 453:653-6. 2008
    ....
  26. pmc Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin
    Fumio Inagaki
    Subground Animalcule Retrieval Project, Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, Yokosuka 237 0061, Japan
    Proc Natl Acad Sci U S A 103:2815-20. 2006
    ..The recognition of which microbial groups prevail under distinctive subseafloor environments is a significant step toward determining the role these communities play in Earth's essential biogeochemical processes...
  27. ncbi Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin
    Kyle C Costa
    School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
    Extremophiles 13:447-59. 2009
    ....
  28. ncbi Distributions of microbial activities in deep subseafloor sediments
    Steven D'Hondt
    Ocean Drilling Program Leg 201 Shipboard Scientific Party, NASA Astrobiology Institute, University of Rhode Island Graduate School of Oceanography, South Ferry Road, Narragansett, RI 02882, USA
    Science 306:2216-21. 2004
    ..In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere...
  29. pmc Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities
    Alban Ramette
    Microbial habitat group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Appl Environ Microbiol 75:2495-505. 2009
    ..The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed...
  30. pmc Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments
    Kyoko Kubo
    Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    ISME J 6:1949-65. 2012
    ..This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes...
  31. pmc The effects of hypoxia on sediment nitrogen cycling in the Baltic Sea
    Helena Jäntti
    Department of Environmental Sciences, Aquatic Sciences, University of Helsinki, Finland
    Ambio 41:161-9. 2012
    ..The nitrogen removal rates measured in this study show that nitrogen removal has decreased in the Gulf of Finland compared to rates measured in mid-1990s and the decrease is most likely caused by the increased bottom water hypoxia...
  32. ncbi Evidence for complete denitrification in a benthic foraminifer
    Nils Risgaard-Petersen
    Department of Marine Ecology, National Environmental Research Institute, Vejlsøvej 25, DK 8600 Silkeborg, Denmark
    Nature 443:93-6. 2006
    ....
  33. pmc Mangrove trees affect the community structure and distribution of anammox bacteria at an anthropogenic-polluted mangrove in the Pearl River Delta reflected by 16S rRNA and hydrazine oxidoreductase (HZO) encoding gene analyses
    Meng Li
    School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People s Republic of China
    Ecotoxicology 20:1780-90. 2011
    ..In addition, the correlation analysis showed the redox potential and the molar ratio of ammonium to nitrite in sediments might be important factors affecting the diversity and distribution of anammox bacteria in mangrove sediments...
  34. ncbi A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments
    Meng Li
    Division of Microbiology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People s Republic of China
    Appl Microbiol Biotechnol 86:781-90. 2010
    ..Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem...
  35. pmc Diversity and distribution of methanotrophic archaea at cold seeps
    Katrin Knittel
    Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Celsiusstrasse 1, 28359 Bremen, Germany
    Appl Environ Microbiol 71:467-79. 2005
    ..These variations in the distribution, diversity, and morphology of methanotrophic consortia are discussed with respect to the presence of microbial ecotypes, niche formation, and biogeography...
  36. pmc Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments
    V J Orphan
    Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, P O Box 628, Moss Landing, California 95039
    Appl Environ Microbiol 67:1922-34. 2001
    ....
  37. ncbi Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade
    Lars Schreiber
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Environ Microbiol 12:2327-40. 2010
    ..SEEP-SRB1a contributed to only 0.3% to 0.7% of all single cells in almost all samples indicating that these bacteria are highly adapted to a symbiotic relationship with ANME-2...
  38. ncbi Impact of humans on the flux of terrestrial sediment to the global coastal ocean
    James P M Syvitski
    Environmental Computation and Imaging Facility, Institute of Arctic and Alpine Research INSTAAR, University of Colorado, Boulder, CO 80309 0450, USA
    Science 308:376-80. 2005
    ..African and Asian rivers carry a greatly reduced sediment load; Indonesian rivers deliver much more sediment to coastal areas...
  39. ncbi Streptomyces xiamenensis sp. nov., isolated from mangrove sediment
    Jun Xu
    Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
    Int J Syst Evol Microbiol 59:472-6. 2009
    ..38 %. Based on its phenotypic and genotypic characteristics, strain MCCC 1A01550(T) (=DSM 41903(T)=CGMCC 4.3534(T)) represents the type strain of a novel species, for which the name Streptomyces xiamenensis sp. nov. is proposed...
  40. ncbi Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink
    Helge Niemann
    Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
    Nature 443:854-8. 2006
    ..This mechanism limits the capacity of the microbial methane filter at active marine mud volcanoes to <40% of the total flux...
  41. pmc Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments
    C Vetriani
    Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901 8521, USA
    Appl Environ Microbiol 65:4375-84. 1999
    ..Comparative denaturing gradient gel electrophoresis profile analysis of archaeal 16S rDNA V3 fragments revealed a significant depth-related variability in the composition of the archaeal population...
  42. ncbi Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera
    T J Vick
    University of Nevada, Las Vegas, USA
    Geobiology 8:140-54. 2010
    ..The results indicate that springs associated with the Long Valley Caldera contain microbial populations that show some similarities both to springs in Yellowstone and springs in the Great Basin...
  43. ncbi The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal tar-contaminated sediment, reveals physiological and metabolic versatility and evolution through extensive horizontal gene transfer
    Jane M Yagi
    Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
    Environ Microbiol 11:2253-70. 2009
    ..These new phenotypes and genotypes set the stage for gaining additional insights into the physiology and biochemistry contributing to strain CJ2's fitness in its native habitat, contaminated sediment...
  44. ncbi Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia
    Jane M Caffrey
    Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL, USA
    ISME J 1:660-2. 2007
    ..This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history...
  45. ncbi Extinction and ecosystem function in the marine benthos
    Martin Solan
    Oceanlab, University of Aberdeen, Main Street, Newburgh, Aberdeenshire, Scotland AB41 6AA
    Science 306:1177-80. 2004
    ..As a result, the particular cause of extinction and the order in which species are lost ultimately govern the ecosystem-level consequences of biodiversity loss...
  46. ncbi Distribution and speciation of heavy metals in sediments from the mainstream, tributaries, and lakes of the Yangtze River catchment of Wuhan, China
    Zhifeng Yang
    State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
    J Hazard Mater 166:1186-94. 2009
    ..0% from tributaries, and 88.9% from lakes exhibited low and moderate ecological risk of heavy metals, and the potential ecological risks in the mainstream and tributaries were higher than those in lakes...
  47. pmc Environmental factors shape sediment anammox bacterial communities in hypernutrified Jiaozhou Bay, China
    Hongyue Dang
    State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum East China, 66 West Changjiang Rd, Qingdao 266555, China
    Appl Environ Microbiol 76:7036-47. 2010
    ....
  48. pmc Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments
    C Ryan Penton
    Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Sciences Bldg, East Lansing, MI 48824, USA
    Appl Environ Microbiol 72:6829-32. 2006
    ..This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments...
  49. pmc Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment
    Virginia P Edgcomb
    The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
    Proc Natl Acad Sci U S A 99:7658-62. 2002
    ..g., phototrophs) are simply deposited by sedimentary processes. In contrast, bacterial populations in these sediments are primarily characteristic of anoxic, reduced, hydrocarbon-rich sedimentary habitats...
  50. ncbi Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA
    Anders Lanzen
    Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
    FEMS Microbiol Ecol 77:577-89. 2011
    ..Further, predicted diversity from RNA samples was consistently lower than that from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights...
  51. pmc Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments
    Thorsten Stoeck
    Marine Science Center, Northeastern University, East Point, Nahant, MA 01908, USA
    Appl Environ Microbiol 69:2657-63. 2003
    ..This suggests that oxygen-depleted environments harbor diverse communities of novel organisms, which may provide an interesting window into the early evolution of eukaryotes...
  52. ncbi Seasonal dynamics of anammox bacteria in estuarial sediment of the Mai Po Nature Reserve revealed by analyzing the 16S rRNA and hydrazine oxidoreductase (hzo) genes
    Meng Li
    School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China
    Microbes Environ 26:15-22. 2011
    ....
  53. ncbi Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin
    Eva Alexander
    University of Kaiserslautern, School of Biology, Kaiserslautern, Germany
    Environ Microbiol 11:360-81. 2009
    ..The deep hypersaline anoxic basins in the Mediterranean Sea provide an ideal platform to test for this hypothesis and are promising targets for the discovery of undescribed protists with unknown physiological capabilities...
  54. ncbi Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary
    Alyson E Santoro
    Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
    Environ Microbiol 10:1068-79. 2008
    ..These results offer new insights into the ecology of AOA and beta-AOB by elucidating conditions that may favour the numerical dominance of beta-AOB over AOA in coastal sediments...
  55. pmc Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California
    Scott D Wankel
    Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
    Appl Environ Microbiol 77:269-80. 2011
    ..This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments...
  56. pmc Global occurrence of archaeal amoA genes in terrestrial hot springs
    Chuanlun L Zhang
    Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
    Appl Environ Microbiol 74:6417-26. 2008
    ..Our study demonstrates the global occurrence of putative archaeal amoA genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA...
  57. ncbi Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia
    Anne E Dekas
    Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
    Science 326:422-6. 2009
    ..This finding extends the demonstrated lower limits of respiratory energy capable of fueling N2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles...
  58. pmc Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea
    Tina Lösekann
    Max Planck Institute for Marine Microbiology, Celsiusstr 1, 28359 Bremen, Germany
    Appl Environ Microbiol 73:3348-62. 2007
    ..Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and anaerobic methanotrophs...
  59. ncbi Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands
    Simone I Böer
    Microbial habitat group, Max Planck Institute for Marine Microbiology, Bremen, Germany
    ISME J 3:780-91. 2009
    ..Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities...
  60. ncbi Manganese- and iron-dependent marine methane oxidation
    Emily J Beal
    Department of Geosciences and Penn State Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA
    Science 325:184-7. 2009
    ..Large amounts of manganese and iron are provided to oceans from rivers, indicating that manganese- and iron-dependent AOM have the potential to be globally important...
  61. ncbi Oceanic methane biogeochemistry
    William S Reeburgh
    Department of Earth System Science, University of California, Irvine, California 92697 3100, USA
    Chem Rev 107:486-513. 2007
  62. ncbi Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches
    Victoria J Bertics
    Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
    ISME J 3:1269-85. 2009
    ..Our study provides implications on the community structure of microbial communities in marine sediments and the factors controlling their distribution...
  63. ncbi A constant flux of diverse thermophilic bacteria into the cold Arctic seabed
    Casey Hubert
    Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Science 325:1541-4. 2009
    ..These transport pathways may broadly influence microbial community composition in the marine environment...
  64. pmc Global distribution and diversity of marine Verrucomicrobia
    Sara Freitas
    Department of Earth System Science, University of California Irvine, CA 92697, USA
    ISME J 6:1499-505. 2012
    ..Although we still know little about the ecophysiology of Verrucomicrobia lineages, the ubiquity of this phylum suggests that it may be important for the biogeochemical cycle of carbon in the ocean...
  65. pmc Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China
    Shuai Liu
    Department of Environmental Engineering, Zhejiang University, Hangzhou, China
    Appl Environ Microbiol 79:4065-71. 2013
    ....
  66. ncbi Assessment of heavy metal contamination in Hindon River sediments: a chemometric and geochemical approach
    Mayuri Chabukdhara
    Environmental Engineering Laboratory, Department of Civil Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110 016, India
    Chemosphere 87:945-53. 2012
    ..Consequently, it may serve to undertake and design effective strategies and remedial measures to prevent further deterioration of the river ecosystem in future...
  67. ncbi Cytochrome cd1-containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (Anammox) bacteria
    Meng Li
    School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China
    Environ Sci Technol 45:3547-53. 2011
    ....
  68. pmc Resource quantity affects benthic microbial community structure and growth efficiency in a temperate intertidal mudflat
    Daniel J Mayor
    Institute of Biological and Environmental Sciences, Oceanlab, University of Aberdeen, Aberdeen, United Kingdom
    PLoS ONE 7:e38582. 2012
    ....
  69. ncbi Vertical migration, nitrate uptake and denitrification: survival mechanisms of foraminifers (Globobulimina turgida) under low oxygen conditions
    Karoliina A Koho
    Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
    FEMS Microbiol Ecol 75:273-83. 2011
    ....
  70. pmc Integrated assessment of heavy metal contamination in sediments from a coastal industrial basin, NE China
    Xiaoyu Li
    State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Xinjiang, China
    PLoS ONE 7:e39690. 2012
    ....
  71. ncbi Single-cell analysis reveals a novel uncultivated magnetotactic bacterium within the candidate division OP3
    Sebastian Kolinko
    Ludwig Maximilians Universitat Munich, Microbiology, Großhaderner Strasse 2 4, Planegg Martinsried, Germany
    Environ Microbiol 14:1709-21. 2012
    ..SKK-01 represents the first morphotype that can be assigned to the OP3 group as well as the first magnetotactic member of the PVC superphylum...
  72. ncbi Potential methane reservoirs beneath Antarctica
    J L Wadham
    School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
    Nature 488:633-7. 2012
    ..Our findings suggest that the Antarctic Ice Sheet may be a neglected but important component of the global methane budget, with the potential to act as a positive feedback on climate warming during ice-sheet wastage...
  73. pmc Ocean currents shape the microbiome of Arctic marine sediments
    Leila J Hamdan
    Marine Biogeochemistry Section, Code 6114, US Naval Research Laboratory, Washington DC 20375, USA
    ISME J 7:685-96. 2013
    ..This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane...
  74. ncbi Polycyclic aromatic hydrocarbons (PAHs) in surface sediment and oysters (Crassostrea rhizophorae) from mangrove of Guadeloupe: levels, bioavailability, and effects
    Gaëlle Ramdine
    Laboratoire de Biologie Marine, DYNECAR EA926, Universite des Antilles et de la Guyane, Campus de Fouillole BP 592, 97159 Pointe à Pitre cedex, Guadeloupe
    Ecotoxicol Environ Saf 79:80-9. 2012
    ..These data also indicate the need for regular environmental follow-up studies in Guadeloupe...
  75. ncbi Triazole and dihydroimidazole alkaloids from the marine sediment-derived fungus Penicillium paneum SD-44
    Chun Shun Li
    Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, People s Republic of China
    J Nat Prod 74:1331-4. 2011
    ..The cytotoxicity of compounds 1 and 4 and the antimicrobial activity of 1-4 were evaluated...
  76. pmc Environment-dependent distribution of the sediment nifH-harboring microbiota in the Northern South China Sea
    Hongyue Dang
    State Key Laboratory of Heavy Oil Processing, Key Laboratory of Bioengineering and Biotechnology in Universities of Shandong, Centre for Bioengineering and Biotechnology, China University of Petroleum East China, Qingdao, China
    Appl Environ Microbiol 79:121-32. 2013
    ....
  77. ncbi A cultured greigite-producing magnetotactic bacterium in a novel group of sulfate-reducing bacteria
    Christopher T Lefèvre
    Laboratoire de Bioenergetique Cellulaire, UMR 6191, Commissariat à l Energie Atomique Cadarache, Direction des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologie, Saint Paul lez Durance, France
    Science 334:1720-3. 2011
    ..Genomic analysis of BW-1 reveals the presence of two different magnetosome gene clusters, suggesting that one may be responsible for greigite biomineralization and the other for magnetite...
  78. ncbi Biogeographical distribution of diverse anaerobic ammonium oxidizing (anammox) bacteria in Cape Fear River Estuary
    Olivia R Dale
    Department of Biology and Marine Biology, University of North Carolina Wilmington, NC 28403, USA
    Environ Microbiol 11:1194-207. 2009
    ..Thus, we demonstrated a biogeographical distribution of diverse anammox bacteria influenced by salinity, and provide evidence to link anammox abundance and activities in estuarine sediments...
  79. pmc Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments
    Victoria J Orphan
    Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
    Proc Natl Acad Sci U S A 99:7663-8. 2002
    ..Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia...
  80. ncbi Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park
    D Arcy R Meyer-Dombard
    Department of Earth, Atmospheric, and Environmental Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
    Environ Microbiol 13:2216-31. 2011
    ..Here, we present a novel view of SBC formation and variability in hydrothermal ecosystems...
  81. pmc Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill
    Melanie J Beazley
    Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
    PLoS ONE 7:e41305. 2012
    ..The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems...
  82. pmc Marine biodiversity-ecosystem functions under uncertain environmental futures
    Mark T Bulling
    Oceanlab, University of Aberdeen, Main Street, Newburgh, Aberdeenshire AB41 6AA, UK
    Philos Trans R Soc Lond B Biol Sci 365:2107-16. 2010
    ....
  83. ncbi Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan
    Kyoko Kubo
    Max Planck Institute for Marine Microbiology, Bremen, Germany
    Syst Appl Microbiol 34:293-302. 2011
    ..act as highly efficient scavengers of oxygen from the spring water, thus creating a favorable, anoxic environment for Chloroflexus and Thermodesulfobacterium/Thermodesulfatator in deeper layers...
  84. ncbi Tetracycline resistance genes persist at aquaculture farms in the absence of selection pressure
    Manu Tamminen
    Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
    Environ Sci Technol 45:386-91. 2011
    ....
  85. ncbi Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea
    Hongyue Dang
    Centre for Bioengineering and Biotechnology, China University of Petroleum East China, Qingdao 266555, China
    Microbiology 154:2084-95. 2008
    ..Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path...
  86. ncbi Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems
    Erwan G Roussel
    Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Universite de Bretagne Occidentale, IFREMER, CNRS, Institut Universitaire Europeen de la Mer, Plouzane, France
    FEMS Microbiol Ecol 77:647-65. 2011
    ....
  87. ncbi Bioturbators enhance ecosystem function through complex biogeochemical interactions
    Andrew M Lohrer
    National Institute of Water and Atmospheric Research, PO Box 11 115, Hillcrest, Hamilton, New Zealand
    Nature 431:1092-5. 2004
    ..Declines of spatangoid urchins after trawling are well documented, and our research linking these bioturbators to important benthic-pelagic fluxes highlights potential ramifications for productivity in coastal oceans...
  88. pmc Positive feedbacks in seagrass ecosystems--evidence from large-scale empirical data
    Tjisse van der Heide
    Community and Conservation Ecology Group, Centre for Ecological and Evolutionary Studies, Groningen University, Haren, The Netherlands
    PLoS ONE 6:e16504. 2011
    ..Our study demonstrates the potentials of SEM to identify and quantify positive feedbacks mechanisms for ecosystems and other complex systems...
  89. ncbi Phylogenetic diversity of archaeal 16S rRNA and ammonia monooxygenase genes from tropical estuarine sediments on the central west coast of India
    Sanjay K Singh
    National Institute of Oceanography, Dona Paula, Goa 403 004, India
    Res Microbiol 161:177-86. 2010
    ..Also, the diversity of AamoA sequences was higher in Mandovi sediments than those from Zuari and other tropical and/or temperate estuaries studied previously...
  90. ncbi Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin
    Erwan G Roussel
    Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Universite de Bretagne Occidentale, IFREMER, France
    Environ Microbiol 11:2446-62. 2009
    ..This study shows a transition between surface and subsurface sediment archaeal communities...
  91. ncbi An assessment of selected trace elements in intertidal surface sediments collected from the Peninsular Malaysia
    Syaizwan Zahmir Zulkifli
    Center for International Cooperation, Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo, 164 8639, Japan
    Environ Monit Assess 169:457-72. 2010
    ..It is necessary for Malaysia to develop an ISQG for effective quick screening and evaluation of the coastal environment of Peninsular Malaysia...
  92. pmc Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea
    Brandon K Swan
    Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106 9630, USA
    Appl Environ Microbiol 76:757-68. 2010
    ..The differential response of archaeal and bacterial communities to salinity and carbon patterns is consistent with the hypothesis that adaptations to energy stress and availability distinguish the ecologies of these domains...
  93. pmc Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing
    Molly C Redmond
    Graduate Program in Marine Science, University of California, Santa Barbara, CA 93106, USA
    Appl Environ Microbiol 76:6412-22. 2010
    ..This study identifies several bacterial lineages as participants in the oxidation of gaseous hydrocarbons in marine seeps and supports the idea of an alternate function for some pmoA-like genes...
  94. ncbi Evidence for anaerobic syntrophic acetate oxidation during methane production in the profundal sediment of subtropical Lake Kinneret (Israel)
    B Nüsslein
    Max Planck Institut fur terrestrische Mikrobiologie, Karl von Frisch Strasse, D 35043 Marburg, Germany
    Environ Microbiol 3:460-70. 2001
    ....
  95. ncbi Factors affecting benthic impacts at Scottish fish farms
    Daniel J Mayor
    Institute of Biological and Environmental Sciences, Oceanlab, University ofAberdeen, Main Street, Newburgh, Aberdeenshire, Scotland AB41 6AA, UK
    Environ Sci Technol 44:2079-84. 2010
    ....
  96. ncbi Calibration of sulfate levels in the archean ocean
    Kirsten S Habicht
    Danish Center for Earth System Science and Institute of Biology, University of Southern Denmark, Campusvej 55, DK 5230, Odense M, Denmark
    Science 298:2372-4. 2002
    ..Such low sulfate concentrations were maintained by volcanic outgassing of SO2 gas, and severely suppressed sulfate reduction rates allowed for a carbon cycle dominated by methanogenesis...
  97. pmc Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments
    A M Costello
    Environmental Engineering Science 138 78, California Institute of Technology, Pasadena, California 91125, USA
    Appl Environ Microbiol 65:5066-74. 1999
    ..In addition to these findings, 16S rRNA data obtained in this study were combined with previously described phylogenetic data in order to identify operational taxonomic units that can be used to identify methanotrophs at the genus level...
  98. ncbi Heavy metal sources and associated risk in response to agricultural intensification in the estuarine sediments of Chaohu Lake Valley, East China
    Wenzhong Tang
    State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
    J Hazard Mater 176:945-51. 2010
    ..Therefore, heavy metal pollution due to agricultural intensification in Chaohu Lake Valley should be taken into account during the formation of valley management strategies for the water environment...
  99. ncbi Nitrogen-fixing phylotypes of Chesapeake Bay and Neuse River estuary sediments
    J A Burns
    Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
    Microb Ecol 44:336-43. 2002
    ..Differences in environmental site characteristics appear to select for different types of sediment diazotrophs, which is reflected in the phylogenetic composition of amplified nifH sequences...
  100. pmc Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico
    Liyou Wu
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 74:4516-29. 2008
    ....
  101. ncbi A review of factors affecting the release and bioavailability of contaminants during sediment disturbance events
    Jacqueline Eggleton
    Centre for Environment, Fisheries and Aquaculture Science Cefas, Remembrance Avenue, Burnham on Crouch, Essex CM0 8HA, UK
    Environ Int 30:973-80. 2004
    ....

Research Grants9

  1. RECEPTER BINDING PROPERTIES OF CANNABINOID METABOLITES
    Guangdi Wang; Fiscal Year: 2005
    ....
  2. MGB Eclipse Probe Detection of Category A Organisms
    Irina Afonina; Fiscal Year: 2003
    ..In Phase II, we will expand the number of Category A organisms and improve throughput by multiplexing. In addition, commercial prototype MGB Eclipse(TM) probe assays will be developed for each of these organisms. ..
  3. ENZYMOLOGY OF ACETOTROPHIC METHANOGENESIS
    JAMES FERRY; Fiscal Year: 2003
    ..The results are expected to contribute not only to a deeper understanding of the acetate fermentation pathway, but more importantly to the broader field of anaerobic microbiology and beyond. ..
  4. GFP-like proteins:Diversity and determinants of color
    Mikhail Matz; Fiscal Year: 2006
    ..This would greatly facilitate rational design of GFP-like reporters. ..
  5. Fundamental Study of Welding Fume Inhalation
    Serap Erdal; Fiscal Year: 2007
    ..abstract_text> ..
  6. Method Development for the Analysis of PBDEs in Human Placenta Tissue
    An Li; Fiscal Year: 2008
    ..A laboratory procedure is to be developed in order to understand how a wide-spread environmental pollutant affects the health of human fetus before babies are born. [unreadable] [unreadable] [unreadable]..
  7. Beyond GFP and aequorin: Ocean-wide study of fluorescent and luminous proteins
    Mikhail Matz; Fiscal Year: 2009
    ..e., sharing no homology with the previously cloned ones) genetically encoded fluorescent and luminescent markers which may become a basis for the new generation of in vivo labeling and detection technologies. ..
  8. Pilot-scale Research of Novel Amendment Delivery for in-situ Sediment Remediation
    Upal Ghosh; Fiscal Year: 2009
    ..This field research will evaluate the effectiveness of a novel approach to alter the binding capacity of sediments to reduce human exposure to such contaminants. ..
  9. Does ArsenicMitigation in BangladeshRaiseExposure to Bacterial and ViralPathogens
    ALEXANDER FRANS VAN GEEN; Fiscal Year: 2010
    ....