Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

[1]  Qigen Liu,et al.  Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond , 2016, Front. Microbiol..

[2]  Yong Liu,et al.  Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States , 2016, Microbial Ecology.

[3]  H. J. Laanbroek,et al.  Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China , 2015, Front. Microbiol..

[4]  H. Cao,et al.  Microbial community changes along the active seepage site of one cold seep in the Red Sea , 2015, Front. Microbiol..

[5]  R. Villemur,et al.  Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii , 2015, Applied and Environmental Microbiology.

[6]  M. Reis,et al.  Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment , 2015, PloS one.

[7]  Yong Liu,et al.  Distribution of sediment ammonia-oxidizing microorganisms in plateau freshwater lakes , 2015, Applied Microbiology and Biotechnology.

[8]  Yong-Feng Wang,et al.  Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China , 2014, Ecotoxicology.

[9]  Xiao-hong Zhou,et al.  Abundance and Diversity of Ammonia-Oxidizing Microorganisms in the Sediments of Jinshan Lake , 2014, Current Microbiology.

[10]  M. Bayani Cardenas,et al.  Lateral hyporheic exchange throughout the Mississippi River network , 2014 .

[11]  Jack A. Gilbert,et al.  Human and Environmental Impacts on River Sediment Microbial Communities , 2014, PloS one.

[12]  Jorge Rosas,et al.  Determination of Hydraulic Conductivity from Grain‐Size Distribution for Different Depositional Environments , 2014, Ground water.

[13]  Yong Liu,et al.  Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland , 2014, Applied Microbiology and Biotechnology.

[14]  Yong Liu,et al.  Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland , 2014, Applied Microbiology and Biotechnology.

[15]  Liuyan Yang,et al.  Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China , 2014 .

[16]  Xiao-ming Lu,et al.  Characterization of Bacterial Communities in Sediments Receiving Various Wastewater Effluents with High-Throughput Sequencing Analysis , 2014, Microbial Ecology.

[17]  Xiaoyan Wang,et al.  Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils , 2014, Applied Microbiology and Biotechnology.

[18]  T. Datry,et al.  Influence of hyporheic zone characteristics on the structure and activity of microbial assemblages , 2013 .

[19]  S. Schiff,et al.  Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada , 2013, Applied and Environmental Microbiology.

[20]  Y. Sako,et al.  Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov. , 2013, International journal of systematic and evolutionary microbiology.

[21]  Natalia N. Ivanova,et al.  Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.

[22]  Rui Huang,et al.  Vertical Distribution of Ammonia-Oxidizing Archaea and Bacteria in Sediments of a Eutrophic Lake , 2013, Current Microbiology.

[23]  J. Geist,et al.  The effects of stream substratum texture on interstitial conditions and bacterial biofilms: Methodological strategies , 2013 .

[24]  H. Cao,et al.  Global Ecological Pattern of Ammonia-Oxidizing Archaea , 2013, PloS one.

[25]  J. Kelly,et al.  Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers , 2013, Applied and Environmental Microbiology.

[26]  R. González‐Pinzón,et al.  Coupled transport and reaction kinetics control the nitrate source‐sink function of hyporheic zones , 2012 .

[27]  Z. Quan,et al.  Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary , 2012, Journal of Zhejiang University SCIENCE B.

[28]  Rui Huang,et al.  Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu. , 2012, Canadian journal of microbiology.

[29]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[30]  Cheng Cheng,et al.  Horizontal hydraulic conductivity of shallow streambed sediments and comparison with the grain‐size analysis results , 2012 .

[31]  D. Williams,et al.  Bacterial community dynamics in the hyporheic zone of an intermittent stream , 2011, The ISME Journal.

[32]  Sabine Sauvage,et al.  The role of organisms in hyporheic processes: gaps in current knowledge, needs for future research and applications , 2012 .

[33]  C. Médigue,et al.  Complete Genome Sequence of the Chloromethane-Degrading Hyphomicrobium sp. Strain MC1 , 2011, Journal of bacteriology.

[34]  David M. Hannah,et al.  Inter‐disciplinary perspectives on processes in the hyporheic zone , 2011 .

[35]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

[36]  W. D. de Vos,et al.  Genome Sequence of Chthoniobacter flavus Ellin428, an Aerobic Heterotrophic Soil Bacterium , 2011, Journal of bacteriology.

[37]  Alan Agresti,et al.  Categorical Data Analysis , 2003 .

[38]  Y. Bashan,et al.  Heterotrophic cultures of microalgae: metabolism and potential products. , 2011, Water research.

[39]  Thibault Datry,et al.  Influence of streambed sediment clogging on microbial processes in the hyporheic zone , 2010 .

[40]  Ji‐Zheng He,et al.  Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. , 2010, FEMS microbiology ecology.

[41]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[42]  J. Stanford,et al.  Ecology and management of the hyporheic zone: stream–groundwater interactions of running waters and their floodplains , 2010, Journal of the North American Benthological Society.

[43]  D. Williams,et al.  Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments , 2010, Hydrobiologia.

[44]  D. Stahl,et al.  Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria , 2009, Nature.

[45]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[46]  W. Verstraete,et al.  Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. , 2009, FEMS microbiology reviews.

[47]  Jack A. Stanford,et al.  Habitat Heterogeneity and Associated Microbial Community Structure in a Small-Scale Floodplain Hyporheic Flow Path , 2009, Microbial Ecology.

[48]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[49]  H. J. Laanbroek,et al.  Niche separation of ammonia-oxidizing bacteria across a tidal freshwater marsh. , 2008, Environmental microbiology.

[50]  S. Allison,et al.  Resistance, resilience, and redundancy in microbial communities , 2008, Proceedings of the National Academy of Sciences.

[51]  Guanpin Yang,et al.  Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. , 2008, Microbiology.

[52]  Christian Ritz,et al.  qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis , 2008, Bioinform..

[53]  Jordi Moya-Laraño,et al.  Plotting partial correlation and regression in ecological studies , 2008 .

[54]  Aaron Marc Saunders,et al.  Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora , 2008, Applied and Environmental Microbiology.

[55]  B. Ward,et al.  Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. , 2007, Environmental microbiology.

[56]  Adrian E. Raftery,et al.  Bayesian Regularization for Normal Mixture Estimation and Model-Based Clustering , 2007, J. Classif..

[57]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[58]  A. Hill,et al.  Influence of base flow stream bank seepage on riparian zone nitrogen biogeochemistry , 2007 .

[59]  L. Leff,et al.  The influence of stream sediment particle size on bacterial abundance and community composition , 2007, Aquatic Ecology.

[60]  M. Timmons,et al.  Engineering analysis of the stoichiometry of photoautotrophic, autotrophic, and heterotrophic removal of ammonia-nitrogen in aquaculture systems , 2006 .

[61]  D. Williams,et al.  Nitrogen processing in the hyporheic zone of a pastoral stream , 2004 .

[62]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[63]  A. Peacock,et al.  Biogeochemical processes and microbial characteristics across groundwater-surface water boundaries of the Hanford Reach of the Columbia River. , 2003, Environmental science & technology.

[64]  Colin R. Townsend,et al.  Hyporheic community composition in a gravel‐bed stream: influence of vertical hydrological exchange, sediment structure and physicochemistry , 2003 .

[65]  D. Gutknecht,et al.  Clogging Processes in Hyporheic Interstices of an Impounded River, the Danube at Vienna, Austria , 2003 .

[66]  William H. McDowell,et al.  Biogeochemical Hot Spots and Hot Moments at the Interface of Terrestrial and Aquatic Ecosystems , 2003, Ecosystems.

[67]  S. Gayraud,et al.  Influence of Bed‐Sediment Features on the Interstitial Habitat Available for Macroinvertebrates in 15 French Streams , 2003 .

[68]  R. Sinsabaugh,et al.  The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil , 2002 .

[69]  Eric R. Ziegel,et al.  Generalized Linear Models , 2002, Technometrics.

[70]  G. De’ath.  MULTIVARIATE REGRESSION TREES: A NEW TECHNIQUE FOR MODELING SPECIES–ENVIRONMENT RELATIONSHIPS , 2002 .

[71]  Neil Hunter,et al.  Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. , 2002, Microbiology.

[72]  T. Pape,et al.  Laser-diffraction and pipette-method grain sizing of Dutch sediments: correlations for fine fractions of marine, fluvial, and loess samples , 2001, Netherlands Journal of Geosciences - Geologie en Mijnbouw.

[73]  A. Planty‐Tabacchi,et al.  Geomorphic control of denitrification in large river floodplain soils , 2000 .

[74]  F. Triska,et al.  Nitrogen biogeochemistry and surface-subsurface exchange in streams , 2000 .

[75]  A. Franzluebbers,et al.  Assessing biological soil quality with chloroform fumigation-incubation: Why subtract a control? , 1999 .

[76]  A. Franzluebbers,et al.  Relationships of chloroform fumigation-incubation to soil organic matter pools , 1999 .

[77]  Emily H. Stanley,et al.  THE FUNCTIONAL SIGNIFICANCE OF THE HYPORHEIC ZONE IN STREAMS AND RIVERS , 1998 .

[78]  Adrian E. Raftery,et al.  How Many Clusters? Which Clustering Method? Answers Via Model-Based Cluster Analysis , 1998, Comput. J..

[79]  David L. Strayer,et al.  Oxygen, organic matter, and sediment granulometry as controls on hyporheic animal communities , 1997 .

[80]  Jeremy B. Jones,et al.  Surface-subsurface interactions in stream ecosystems. , 1996, Trends in ecology & evolution.

[81]  A. Miall.  The Geology of Fluvial Deposits: Sedimentary Facies, Basin Analysis, and Petroleum Geology , 1996 .

[82]  S. Findlay.  Importance of surface‐subsurface exchange in stream ecosystems: The hyporheic zone , 1995 .

[83]  John G. McPherson,et al.  Alluvial fans and their natural distinction from rivers based on morphology , 1995 .

[84]  S. Fisher,et al.  Parafluvial Nitrogen Dynamics in a Desert Stream Ecosystem , 1994, Journal of the North American Benthological Society.

[85]  J. Bravard,et al.  6 – Geomorphology of Alluvial Groundwater Ecosystems , 1994 .

[86]  M. Pusch,et al.  Community respiration in hyporheic sediments of a mountain stream (Steina, Black Forest) , 1994 .

[87]  David S. White,et al.  Perspectives on Defining and Delineating Hyporheic Zones , 1993, Journal of the North American Benthological Society.

[88]  S. Zeger,et al.  Multivariate Regression Analyses for Categorical Data , 1992 .

[89]  G. Demaison.  Anoxia vs. Productivity: What Controls the Formation of Organic-Carbon-Rich Sediments and Sedimentary Rocks?: Discussion , 1991 .

[90]  F. Triska,et al.  Denitrification in sediments from the hyporheic zone adjacent to a small forested stream , 1990 .

[91]  Russell G. Shepherd,et al.  Correlations of Permeability and Grain Size , 1989 .

[92]  A. Horowitz,et al.  The relation of stream sediment surface area, grain size and composition to trace element chemistry , 1987 .

[93]  I. N. McCave,et al.  Evaluation of a Laser-Diffraction-Size Analyzer for Use with Natural Sediments: RESEARCH METHOD PAPER , 1986 .

[94]  T. Bott,et al.  Bacterial Biomass, Metabolic State, and Activity in Stream Sediments: Relation to Environmental Variables and Multiple Assay Comparisons , 1985, Applied and environmental microbiology.

[95]  M. Deflaun,et al.  Relationships between bacteria and grain surfaces in intertidal sediments1 , 1983 .

[96]  G. Chamberlain.  Multivariate regression models for panel data , 1982 .

[97]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

[98]  W. Wiebe,et al.  Heterotrophic activity associated with particulate size fractions in a Spartina alterniflora salt-marsh estuary, Sapelo Island, Georgia, USA, and the continental shelf waters , 1977 .

[99]  H. Akaike.  A new look at the statistical model identification , 1974 .

[100]  Takeshi Amemiya,et al.  Multivariate Regression and Simultaneous Equation Models when the Dependent Variables Are Truncated Normal , 1974 .

[101]  R. Folk,et al.  Brazos River bar [Texas]; a study in the significance of grain size parameters , 1957 .

[102]  Robert L. Folk,et al.  The Distinction between Grain Size and Mineral Composition in Sedimentary-Rock Nomenclature , 1954, The Journal of Geology.

[103]  W. C. Krumbein,et al.  Permeability as a Function of the Size Parameters of Unconsolidated Sand , 1943 .

[104]  W. C. Krumbein,et al.  Size frequency distributions of sediments and the normal phi curve , 1938 .

[105]  H. J. Fraser.  Experimental Study of the Porosity and Permeability of Clastic Sediments , 1935, The Journal of Geology.

[106]  C. Wentworth.  A Scale of Grade and Class Terms for Clastic Sediments , 1922, The Journal of Geology.

[107]  J. A. Udden.  Mechanical composition of clastic sediments , 1914 .