Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities
- Authors:
-
- Oregon State Univ., Corvallis, OR (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Univ. of Washington, Seattle, WA (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1474503
- Alternate Identifier(s):
- OSTI ID: 1488816
- Report Number(s):
- LLNL-JRNL-741426
Journal ID: ISSN 1664-302X
- Grant/Contract Number:
- AC05-00OR22725; AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: n/a; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological and medical sciences
Citation Formats
Kieft, Brandon, Li, Zhou, Bryson, Samuel, Crump, Byron C., Hettich, Robert, Pan, Chongle, Mayali, Xavier, and Mueller, Ryan S.. Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities. United States: N. p., 2018.
Web. doi:10.3389/fmicb.2018.01282.
Kieft, Brandon, Li, Zhou, Bryson, Samuel, Crump, Byron C., Hettich, Robert, Pan, Chongle, Mayali, Xavier, & Mueller, Ryan S.. Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities. United States. https://doi.org/10.3389/fmicb.2018.01282
Kieft, Brandon, Li, Zhou, Bryson, Samuel, Crump, Byron C., Hettich, Robert, Pan, Chongle, Mayali, Xavier, and Mueller, Ryan S.. Thu .
"Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities". United States. https://doi.org/10.3389/fmicb.2018.01282. https://www.osti.gov/servlets/purl/1474503.
@article{osti_1474503,
title = {Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities},
author = {Kieft, Brandon and Li, Zhou and Bryson, Samuel and Crump, Byron C. and Hettich, Robert and Pan, Chongle and Mayali, Xavier and Mueller, Ryan S.},
abstractNote = {},
doi = {10.3389/fmicb.2018.01282},
journal = {Frontiers in Microbiology},
number = n/a,
volume = 9,
place = {United States},
year = {Thu Jun 14 00:00:00 EDT 2018},
month = {Thu Jun 14 00:00:00 EDT 2018}
}
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Cited by: 29 works
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Figures / Tables:
Table 1.: Genes in Rhodobacterales and Flavobacteriales lineages that are under putative positive selection. OG = orthologous group, where the 3-digit numbers represent clusters of orthologs predicted by ProteinOrtho. P-value = p-value from modeling. Q-value = Benjamin-Hochberg correction of p-values with FDR cut-off set at 0.05. In the COG cat.more »
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Works referenced in this record:
Linking biochemical properties of particles to particle-attached and free-living bacterial community structure along the particle density gradient from freshwater to open ocean: Linking POM to Particle-Attached and Free-Living Bacteria
journal, August 2016
- Zhang, Yao; Xiao, Wei; Jiao, Nianzhi
- Journal of Geophysical Research: Biogeosciences, Vol. 121, Issue 8
STAMP: statistical analysis of taxonomic and functional profiles
journal, July 2014
- Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip
- Bioinformatics, Vol. 30, Issue 21
Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries
journal, March 2002
- Bouvier, Thierry C.; del Giorgio, Paul A.
- Limnology and Oceanography, Vol. 47, Issue 2
Influence of Salinity on Bacterioplankton Communities from the Brazilian Rain Forest to the Coastal Atlantic Ocean
journal, March 2011
- Silveira, Cynthia B.; Vieira, Ricardo P.; Cardoso, Alexander M.
- PLoS ONE, Vol. 6, Issue 3
Sipros Ensemble improves database searching and filtering for complex metaproteomics
journal, September 2017
- Guo, Xuan; Li, Zhou; Yao, Qiuming
- Bioinformatics, Vol. 34, Issue 5
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
journal, November 2015
- Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer
- Nucleic Acids Research, Vol. 44, Issue D1
Seasonal distributions and turnover of reduced trace gases and hydroxylamine in Yaquina Bay, Oregon
journal, March 1987
- Butler, James H.; Jones, Ronald D.; Garber, Jonathan H.
- Geochimica et Cosmochimica Acta, Vol. 51, Issue 3
Molecular characterization of putative biocorroding microbiota with a novel niche detection of Epsilon- and Zetaproteobacteria in Pacific Ocean coastal seawaters: Carbon steel biocorrosion in seawater
journal, September 2011
- Dang, Hongyue; Chen, Ruipeng; Wang, Lin
- Environmental Microbiology, Vol. 13, Issue 11
Development and validation of a habitat suitability model for the non-indigenous seagrass Zostera japonica in North America
journal, January 2016
- Shafer, Deborah; Swannack, Todd; Saltus, Saltus
- Management of Biological Invasions, Vol. 7, Issue 2
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
journal, February 2012
- Wu, Martin; Scott, Alexandra J.
- Bioinformatics, Vol. 28, Issue 7
Gene and translation initiation site prediction in metagenomic sequences
journal, July 2012
- Hyatt, Doug; LoCascio, Philip F.; Hauser, Loren J.
- Bioinformatics, Vol. 28, Issue 17
Sediment-to-water fluxes of particulate material and microbes by resuspension and their contribution to the planktonic food web
journal, January 1990
- Wainright, Sc
- Marine Ecology Progress Series, Vol. 62
Marine metaproteomics: deciphering the microbial metabolic food web
journal, May 2014
- Williams, Timothy J.; Cavicchioli, Ricardo
- Trends in Microbiology, Vol. 22, Issue 5
Metaproteomics of aquatic microbial communities in a deep and stratified estuary
journal, September 2015
- Colatriano, David; Ramachandran, Arthi; Yergeau, Etienne
- PROTEOMICS, Vol. 15, Issue 20
Genetic diversity in Sargasso Sea bacterioplankton
journal, May 1990
- Giovannoni, Stephen J.; Britschgi, Theresa B.; Moyer, Craig L.
- Nature, Vol. 345, Issue 6270
Unexpected Diversity of Bacteria Capable of Carbon Monoxide Oxidation in a Coastal Marine Environment, and Contribution of the Roseobacter-Associated Clade to Total CO Oxidation
journal, March 2006
- Tolli, J. D.; Sievert, S. M.; Taylor, C. D.
- Applied and Environmental Microbiology, Vol. 72, Issue 3
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting
journal, July 2013
- Barnard, Romain L.; Osborne, Catherine A.; Firestone, Mary K.
- The ISME Journal, Vol. 7, Issue 11
Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
journal, February 2016
- Vavourakis, Charlotte D.; Ghai, Rohit; Rodriguez-Valera, Francisco
- Frontiers in Microbiology, Vol. 7
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
journal, January 2005
- Yang, Z.
- Molecular Biology and Evolution, Vol. 22, Issue 4
Particle-attached bacteria and heterotrophic plankton associated with the Columbia River estuarine turbidity maxima
journal, January 1996
- Crump, Bc; Baross, Ja
- Marine Ecology Progress Series, Vol. 138
A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence
journal, April 2010
- Nandi, Tannistha; Ong, Catherine; Singh, Arvind Pratap
- PLoS Pathogens, Vol. 6, Issue 4
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions
journal, January 2009
- Gunbin, Konstantin V.; Afonnikov, Dmitry A.; Kolchanov, Nikolay A.
- BMC Genomics, Vol. 10, Issue 1
Evidence for positive selection on the E2 gene of bovine viral diarrhoea virus type 1
journal, June 2007
- Tang, Fangqiang; Zhang, Chuyu
- Virus Genes, Vol. 35, Issue 3
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011
- Sievers, Fabian; Wilm, Andreas; Dineen, David
- Molecular Systems Biology, Vol. 7, Issue 1
Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon
journal, March 2010
- Poretsky, Rachel S.; Sun, Shulei; Mou, Xiaozhen
- Environmental Microbiology, Vol. 12, Issue 3
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Fast and sensitive protein alignment using DIAMOND
journal, November 2014
- Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
- Nature Methods, Vol. 12, Issue 1
Transformations of nutrients (N, P, Si) in the turbidity maximum zone of the Seine estuary and export to the sea
journal, December 2010
- Garnier, Josette; Billen, Gilles; Némery, Julien
- Estuarine, Coastal and Shelf Science, Vol. 90, Issue 3
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
journal, January 2021
- Karst, Søren M.; Ziels, Ryan M.; Kirkegaard, Rasmus H.
- Nature Methods, Vol. 18, Issue 2
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
journal, May 2006
- Li, W.; Godzik, A.
- Bioinformatics, Vol. 22, Issue 13
Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton
journal, April 2016
- Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer
- mSystems, Vol. 1, Issue 2
Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters
journal, April 2016
- Yung, Cheuk-Man; Ward, Christopher S.; Davis, Katherine M.
- Applied and Environmental Microbiology, Vol. 82, Issue 11
How do divergent ecological strategies emerge among marine bacterioplankton lineages?
journal, September 2015
- Luo, Haiwei; Moran, Mary Ann
- Trends in Microbiology, Vol. 23, Issue 9
Seasonal Variations in the Contributions of Different Bacterial Groups to the Uptake of Low-Molecular-Weight Compounds in Northwestern Mediterranean Coastal Waters
journal, March 2007
- Alonso-Saez, L.; Gasol, J. M.
- Applied and Environmental Microbiology, Vol. 73, Issue 11
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley
journal, March 2015
- Bulgarelli, Davide; Garrido-Oter, Ruben; Münch, Philipp C.
- Cell Host & Microbe, Vol. 17, Issue 3
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
journal, December 2004
- Moran, Mary Ann; Buchan, Alison; González, José M.
- Nature, Vol. 432, Issue 7019
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
Marine Microbes See a Sea of Gradients
journal, November 2012
- Stocker, R.
- Science, Vol. 338, Issue 6107
The changing carbon cycle of the coastal ocean
journal, December 2013
- Bauer, James E.; Cai, Wei-Jun; Raymond, Peter A.
- Nature, Vol. 504, Issue 7478
Bacterial competition: surviving and thriving in the microbial jungle
journal, November 2009
- Hibbing, Michael E.; Fuqua, Clay; Parsek, Matthew R.
- Nature Reviews Microbiology, Vol. 8, Issue 1
New insights into the relationship between taste perception and oral microbiota composition
journal, March 2019
- Cattaneo, Camilla; Gargari, Giorgio; Koirala, Ranjan
- Scientific Reports, Vol. 9, Issue 1
Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time
journal, March 2004
- Crump, B. C.; Hopkinson, C. S.; Sogin, M. L.
- Applied and Environmental Microbiology, Vol. 70, Issue 3
Mating pair stabilization mediates bacterial conjugation species specificity
journal, June 2022
- Low, Wen Wen; Wong, Joshua L. C.; Beltran, Leticia C.
- Nature Microbiology, Vol. 7, Issue 7
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem
journal, January 2013
- Smith, Maria W.; Zeigler Allen, Lisa; Allen, Andrew E.
- Frontiers in Microbiology, Vol. 4
Metaproteomics reveals the major microbial players and their biogeochemical functions in a productive coastal system in the northern South China Sea: Shantou coast microbial metaproteomics
journal, July 2014
- Dong, Hong-Po; Hong, Yi-Guo; Lu, Songhui
- Environmental Microbiology Reports, Vol. 6, Issue 6
The Pfam protein families database: towards a more sustainable future
journal, December 2015
- Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
- Nucleic Acids Research, Vol. 44, Issue D1
The Pfam protein families database: towards a more sustainable future
journal, December 2015
- Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
- Nucleic Acids Research, Vol. 44, Issue D1
An integrative study of a meromictic lake ecosystem in Antarctica
journal, December 2010
- Lauro, Federico M.; DeMaere, Matthew Z.; Yau, Sheree
- The ISME Journal, Vol. 5, Issue 5
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
journal, March 2015
- Nayfach, Stephen; Pollard, Katherine S.
- Genome Biology, Vol. 16, Issue 1
Coupling Between the Coastal Ocean and Yaquina Bay, Oregon: Importance of Oceanic Inputs Relative to Other Nitrogen Sources
journal, January 2009
- Brown, Cheryl A.; Ozretich, Robert J.
- Estuaries and Coasts, Vol. 32, Issue 2
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing
journal, August 2014
- Takahashi, Shunsuke; Tomita, Junko; Nishioka, Kaori
- PLoS ONE, Vol. 9, Issue 8
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
journal, March 2001
- Washburn, Michael P.; Wolters, Dirk; Yates, John R.
- Nature Biotechnology, Vol. 19, Issue 3
Phylogenetically conserved resource partitioning in the coastal microbial loop
journal, August 2017
- Bryson, Samuel; Li, Zhou; Chavez, Francisco
- The ISME Journal, Vol. 11, Issue 12
Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary
journal, January 2016
- Jeffries, Thomas C.; Schmitz Fontes, Maria L.; Harrison, Daniel P.
- Frontiers in Microbiology, Vol. 6
Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison
journal, April 2014
- D'Ambrosio, Lindsay; Ziervogel, Kai; MacGregor, Barbara
- The ISME Journal, Vol. 8, Issue 11
Particulate organic carbon in the estuarine turbidity maxima of the Gironde, Loire and Seine estuaries: origin and lability
journal, September 2007
- Etcheber, Henri; Taillez, Aurélien; Abril, Gwenaël
- Hydrobiologia, Vol. 588, Issue 1
Attached and Free Bacteria in an Estuary with Abundant Suspended Solids
journal, December 1977
- Goulder, R.
- Journal of Applied Bacteriology, Vol. 43, Issue 3
Determination of apparent quantum yield spectra for the formation of biologically labile photoproducts
journal, March 2002
- Miller, William L.; Moran, Miller; Sheldon, Wade M.
- Limnology and Oceanography, Vol. 47, Issue 2
Activity of abundant and rare bacteria in a coastal ocean
journal, July 2011
- Campbell, B. J.; Yu, L.; Heidelberg, J. F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 31
Bacterial Biogeography across the Amazon River-Ocean Continuum
journal, May 2017
- Doherty, Mary; Yager, Patricia L.; Moran, Mary Ann
- Frontiers in Microbiology, Vol. 8
Particle-attached bacteria and heterotrophic plankton associated with the Columbia River estuarine turbidity maxima
journal, January 1996
- Crump, Bc; Baross, Ja
- Marine Ecology Progress Series, Vol. 138
Mechanisms and ecological role of carbon transfer within coastal seascapes: Carbon transfer within coastal seascapes
journal, August 2013
- Hyndes, Glenn A.; Nagelkerken, Ivan; McLeod, Rebecca J.
- Biological Reviews, Vol. 89, Issue 1
Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning
journal, May 2016
- Delgado-Baquerizo, Manuel; Giaramida, Luca; Reich, Peter B.
- Journal of Ecology, Vol. 104, Issue 4
How do divergent ecological strategies emerge among marine bacterioplankton lineages?
journal, September 2015
- Luo, Haiwei; Moran, Mary Ann
- Trends in Microbiology, Vol. 23, Issue 9
Oceanography of the U.S. Pacific Northwest Coastal Ocean and estuaries with application to coastal ecology
journal, August 2003
- Hickey, Barbara M.; Banas, Neil S.
- Estuaries, Vol. 26, Issue 4
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary: POC controls bacterial production
journal, June 2017
- Crump, Byron C.; Fine, Lindy M.; Fortunato, Caroline S.
- Limnology and Oceanography, Vol. 62, Issue 6
A terrestrial organic matter depocenter on a high-energy margin: The Umpqua River system, Oregon
journal, May 2012
- Hastings, R. H.; Goñi, M. A.; Wheatcroft, R. A.
- Continental Shelf Research, Vol. 39-40
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
journal, January 2015
- Laczny, Cedric C.; Sternal, Tomasz; Plugaru, Valentin
- Microbiome, Vol. 3, Issue 1
STAMP: statistical analysis of taxonomic and functional profiles
journal, July 2014
- Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip
- Bioinformatics, Vol. 30, Issue 21
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment
journal, June 2021
- Kim, Minji; Lee, Ki-Eun; Cha, In-Tae
- Current Microbiology, Vol. 78, Issue 8
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
journal, February 2012
- Wu, Martin; Scott, Alexandra J.
- Bioinformatics, Vol. 28, Issue 7
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
journal, November 2015
- Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer
- Nucleic Acids Research, Vol. 44, Issue D1
Phylogenetic Analysis of Particle-Attached and Free-Living Bacterial Communities in the Columbia River, Its Estuary, and the Adjacent Coastal Ocean
journal, July 1999
- Crump, Byron C.; Armbrust, E. Virginia; Baross, John A.
- Applied and Environmental Microbiology, Vol. 65, Issue 7
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
journal, May 2006
- Li, W.; Godzik, A.
- Bioinformatics, Vol. 22, Issue 13
Dominance of particle-attached bacteria in the Columbia River estuary, USA
journal, January 1998
- Crump, Bc; Baross, Ja; Simenstad, Ca
- Aquatic Microbial Ecology, Vol. 14
Carbon Monoxide Photoproduction from Particles and Solutes in the Delaware Estuary under Contrasting Hydrological Conditions
journal, November 2015
- Song, Guisheng; Richardson, John D.; Werner, James P.
- Environmental Science & Technology, Vol. 49, Issue 24
Molecular characterization of putative biocorroding microbiota with a novel niche detection of Epsilon- and Zetaproteobacteria in Pacific Ocean coastal seawaters: Carbon steel biocorrosion in seawater
journal, September 2011
- Dang, Hongyue; Chen, Ruipeng; Wang, Lin
- Environmental Microbiology, Vol. 13, Issue 11
Metatranscriptomic Analyses of Plankton Communities Inhabiting Surface and Subpycnocline Waters of the Chesapeake Bay during Oxic-Anoxic-Oxic Transitions
journal, October 2013
- Hewson, Ian; Eggleston, Erin M.; Doherty, Mary
- Applied and Environmental Microbiology, Vol. 80, Issue 1
Interactome analysis reveals that lncRNA HULC promotes aerobic glycolysis through LDHA and PKM2
journal, June 2020
- Wang, Chunqing; Li, Yongmei; Yan, Shuai
- Nature Communications, Vol. 11, Issue 1
Development and validation of a habitat suitability model for the non-indigenous seagrass Zostera japonica in North America
journal, January 2016
- Shafer, Deborah; Swannack, Todd; Saltus, Saltus
- Management of Biological Invasions, Vol. 7, Issue 2
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
journal, December 2004
- Moran, Mary Ann; Buchan, Alison; González, José M.
- Nature, Vol. 432, Issue 7019
Aerobic Anoxygenic Phototrophic Bacteria Attached to Particles in Turbid Waters of the Delaware and Chesapeake Estuaries
journal, April 2007
- Waidner, L. A.; Kirchman, D. L.
- Applied and Environmental Microbiology, Vol. 73, Issue 12
Sediment-to-water fluxes of particulate material and microbes by resuspension and their contribution to the planktonic food web
journal, January 1990
- Wainright, Sc
- Marine Ecology Progress Series, Vol. 62
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
journal, April 2015
- Baker, Brett J.; Lazar, Cassandre Sara; Teske, Andreas P.
- Microbiome, Vol. 3, Issue 1
Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon
journal, March 2010
- Poretsky, Rachel S.; Sun, Shulei; Mou, Xiaozhen
- Environmental Microbiology, Vol. 12, Issue 3
Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
journal, February 2014
- Dupont, Chris L.; Larsson, John; Yooseph, Shibu
- PLoS ONE, Vol. 9, Issue 2
Spatial and temporal patterns in the Pelagibacteraceae across an estuarine gradient
journal, July 2016
- Ortmann, Alice C.; Santos, Thays T. L.
- FEMS Microbiology Ecology, Vol. 92, Issue 9
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions
journal, January 2009
- Gunbin, Konstantin V.; Afonnikov, Dmitry A.; Kolchanov, Nikolay A.
- BMC Genomics, Vol. 10, Issue 1
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics
journal, January 2015
- Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes
- The ISME Journal, Vol. 9, Issue 7
Phylogenetically conserved resource partitioning in the coastal microbial loop
journal, August 2017
- Bryson, Samuel; Li, Zhou; Chavez, Francisco
- The ISME Journal, Vol. 11, Issue 12
Resistance, resilience, and redundancy in microbial communities
journal, August 2008
- Allison, S. D.; Martiny, J. B. H.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
journal, February 2016
- Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae
- Journal of Molecular Biology, Vol. 428, Issue 4
Metagenome-assembled genomes uncover a global brackish microbiome
journal, December 2015
- Hugerth, Luisa W.; Larsson, John; Alneberg, Johannes
- Genome Biology, Vol. 16, Issue 1
A terrestrial organic matter depocenter on a high-energy margin: The Umpqua River system, Oregon
journal, May 2012
- Hastings, R. H.; Goñi, M. A.; Wheatcroft, R. A.
- Continental Shelf Research, Vol. 39-40
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
journal, January 2005
- Yang, Z.
- Molecular Biology and Evolution, Vol. 22, Issue 4
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
journal, June 2013
- Peng, Yu; Leung, Henry C. M.; Yiu, Siu-Ming
- Bioinformatics, Vol. 29, Issue 13
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015
- Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.
- Bioinformatics, Vol. 32, Issue 4
Gene and translation initiation site prediction in metagenomic sequences
journal, July 2012
- Hyatt, Doug; LoCascio, Philip F.; Hauser, Loren J.
- Bioinformatics, Vol. 28, Issue 17
Marine metaproteomics: deciphering the microbial metabolic food web
journal, May 2014
- Williams, Timothy J.; Cavicchioli, Ricardo
- Trends in Microbiology, Vol. 22, Issue 5
Conservation evaluation and phylogenetic diversity
journal, January 1992
- Faith, Daniel P.
- Biological Conservation, Vol. 61, Issue 1
Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem
journal, September 2014
- Simon, Holly M.; Smith, Maria W.; Herfort, Lydie
- Frontiers in Microbiology, Vol. 5
Genetic diversity in Sargasso Sea bacterioplankton
journal, May 1990
- Giovannoni, Stephen J.; Britschgi, Theresa B.; Moyer, Craig L.
- Nature, Vol. 345, Issue 6270
Seasonal distributions and turnover of reduced trace gases and hydroxylamine in Yaquina Bay, Oregon
journal, March 1987
- Butler, James H.; Jones, Ronald D.; Garber, Jonathan H.
- Geochimica et Cosmochimica Acta, Vol. 51, Issue 3
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016
- Letunic, Ivica; Bork, Peer
- Nucleic Acids Research, Vol. 44, Issue W1
Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes
journal, July 2016
- Cottrell, Matthew T.; Kirchman, David L.
- Applied and Environmental Microbiology, Vol. 82, Issue 19
Microbial Surface Colonization and Biofilm Development in Marine Environments
journal, December 2015
- Dang, Hongyue; Lovell, Charles R.
- Microbiology and Molecular Biology Reviews, Vol. 80, Issue 1
Metagenomic biomarker discovery and explanation
journal, January 2011
- Segata, Nicola; Izard, Jacques; Waldron, Levi
- Genome Biology, Vol. 12, Issue 6
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
journal, March 2001
- Washburn, Michael P.; Wolters, Dirk; Yates, John R.
- Nature Biotechnology, Vol. 19, Issue 3
Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro
journal, August 2004
- Henriques, Isabel S.; Almeida, Adelaide; Cunha, ÃNgela
- FEMS Microbiology Ecology, Vol. 49, Issue 2
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem
journal, January 2013
- Smith, Maria W.; Zeigler Allen, Lisa; Allen, Andrew E.
- Frontiers in Microbiology, Vol. 4
Marine Microbes See a Sea of Gradients
journal, November 2012
- Stocker, R.
- Science, Vol. 338, Issue 6107
Rhizosphere bacteriome structure and functions
journal, February 2022
- Ling, Ning; Wang, Tingting; Kuzyakov, Yakov
- Nature Communications, Vol. 13, Issue 1
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing
journal, August 2014
- Takahashi, Shunsuke; Tomita, Junko; Nishioka, Kaori
- PLoS ONE, Vol. 9, Issue 8
Phylogenetic limiting similarity and competitive exclusion: Phylogenetic relatedness and competition
journal, June 2011
- Violle, Cyrille; Nemergut, Diana R.; Pu, Zhichao
- Ecology Letters, Vol. 14, Issue 8
Carbon in catchments: connecting terrestrial carbon losses with aquatic metabolism
journal, January 2001
- Cole, Jonathan J.; Cole, Jonathan J.; Caraco, Nina F.
- Marine and Freshwater Research, Vol. 52, Issue 1
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009
- Schloss, P. D.; Westcott, S. L.; Ryabin, T.
- Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
2016 update of the PRIDE database and its related tools
journal, November 2015
- Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi
- Nucleic Acids Research, Vol. 44, Issue D1
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary: POC controls bacterial production
journal, June 2017
- Crump, Byron C.; Fine, Lindy M.; Fortunato, Caroline S.
- Limnology and Oceanography, Vol. 62, Issue 6
An integrative study of a meromictic lake ecosystem in Antarctica
journal, December 2010
- Lauro, Federico M.; DeMaere, Matthew Z.; Yau, Sheree
- The ISME Journal, Vol. 5, Issue 5
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley
journal, March 2015
- Bulgarelli, Davide; Garrido-Oter, Ruben; Münch, Philipp C.
- Cell Host & Microbe, Vol. 17, Issue 3
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro
journal, August 2004
- Henriques, Isabel S.; Almeida, Adelaide; Cunha, ÃNgela
- FEMS Microbiology Ecology, Vol. 49, Issue 2
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens
journal, March 2021
- Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W.
- Nature Genetics, Vol. 53, Issue 3
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
journal, May 2000
- Yang, Ziheng; Nielsen, Rasmus; Goldman, Nick
- Genetics, Vol. 155, Issue 1
Bacterial competition: surviving and thriving in the microbial jungle
journal, November 2009
- Hibbing, Michael E.; Fuqua, Clay; Parsek, Matthew R.
- Nature Reviews Microbiology, Vol. 8, Issue 1
Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem
journal, September 2014
- Simon, Holly M.; Smith, Maria W.; Herfort, Lydie
- Frontiers in Microbiology, Vol. 5
Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
journal, February 2014
- Dupont, Chris L.; Larsson, John; Yooseph, Shibu
- PLoS ONE, Vol. 9, Issue 2
A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence
journal, April 2010
- Nandi, Tannistha; Ong, Catherine; Singh, Arvind Pratap
- PLoS Pathogens, Vol. 6, Issue 4
Determination of apparent quantum yield spectra for the formation of biologically labile photoproducts
journal, March 2002
- Miller, William L.; Moran, Miller; Sheldon, Wade M.
- Limnology and Oceanography, Vol. 47, Issue 2
Spatial and temporal patterns in the Pelagibacteraceae across an estuarine gradient
journal, July 2016
- Ortmann, Alice C.; Santos, Thays T. L.
- FEMS Microbiology Ecology, Vol. 92, Issue 9
Attached and Free Bacteria in an Estuary with Abundant Suspended Solids
journal, December 1977
- Goulder, R.
- Journal of Applied Bacteriology, Vol. 43, Issue 3
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011
- Sievers, Fabian; Wilm, Andreas; Dineen, David
- Molecular Systems Biology, Vol. 7, Issue 1
Evidence for positive selection on the E2 gene of bovine viral diarrhoea virus type 1
journal, June 2007
- Tang, Fangqiang; Zhang, Chuyu
- Virus Genes, Vol. 35, Issue 3
Bacterial Biogeography across the Amazon River-Ocean Continuum
journal, May 2017
- Doherty, Mary; Yager, Patricia L.; Moran, Mary Ann
- Frontiers in Microbiology, Vol. 8
Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison
journal, April 2014
- D'Ambrosio, Lindsay; Ziervogel, Kai; MacGregor, Barbara
- The ISME Journal, Vol. 8, Issue 11
Particulate organic carbon in the estuarine turbidity maxima of the Gironde, Loire and Seine estuaries: origin and lability
journal, September 2007
- Etcheber, Henri; Taillez, Aurélien; Abril, Gwenaël
- Hydrobiologia, Vol. 588, Issue 1
Bacterial sulfate reduction within reduced microniches of oxidized marine sediments
journal, January 1977
- J�rgensen, B. B.
- Marine Biology, Vol. 41, Issue 1
Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning
journal, May 2016
- Delgado-Baquerizo, Manuel; Giaramida, Luca; Reich, Peter B.
- Journal of Ecology, Vol. 104, Issue 4
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
journal, April 2015
- Baker, Brett J.; Lazar, Cassandre Sara; Teske, Andreas P.
- Microbiome, Vol. 3, Issue 1
Transformations of nutrients (N, P, Si) in the turbidity maximum zone of the Seine estuary and export to the sea
journal, December 2010
- Garnier, Josette; Billen, Gilles; Némery, Julien
- Estuarine, Coastal and Shelf Science, Vol. 90, Issue 3
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics
journal, January 2015
- Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes
- The ISME Journal, Vol. 9, Issue 7
Proteinortho: Detection of (Co-)orthologs in large-scale analysis
journal, April 2011
- Lechner, Marcus; Findeiß, Sven; Steiner, Lydia
- BMC Bioinformatics, Vol. 12, Issue 1
Carbon Monoxide Photoproduction from Particles and Solutes in the Delaware Estuary under Contrasting Hydrological Conditions
journal, November 2015
- Song, Guisheng; Richardson, John D.; Werner, James P.
- Environmental Science & Technology, Vol. 49, Issue 24
Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary
journal, January 2016
- Jeffries, Thomas C.; Schmitz Fontes, Maria L.; Harrison, Daniel P.
- Frontiers in Microbiology, Vol. 6
Particulate organic matter export by two contrasting small mountainous rivers from the Pacific Northwest, U.S.A.: POM IN CONTRASTING SMALL MOUNTAINOUS RIVERS
journal, February 2013
- Goñi, Miguel A.; Hatten, Jeff A.; Wheatcroft, Robert A.
- Journal of Geophysical Research: Biogeosciences, Vol. 118, Issue 1
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
journal, June 2013
- Peng, Yu; Leung, Henry C. M.; Yiu, Siu-Ming
- Bioinformatics, Vol. 29, Issue 13
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015
- Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.
- Bioinformatics, Vol. 32, Issue 4
Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
journal, November 2001
- Posada, D.; Crandall, K. A.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 24
Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates
journal, January 2008
- Campanaro, Stefano; Treu, Laura; Valle, Giorgio
- BMC Evolutionary Biology, Vol. 8, Issue 1
An alternative polysaccharide uptake mechanism of marine bacteria
journal, March 2017
- Reintjes, Greta; Arnosti, Carol; Fuchs, Bernhard M.
- The ISME Journal, Vol. 11, Issue 7
Coupling Between the Coastal Ocean and Yaquina Bay, Oregon: Importance of Oceanic Inputs Relative to Other Nitrogen Sources
journal, January 2009
- Brown, Cheryl A.; Ozretich, Robert J.
- Estuaries and Coasts, Vol. 32, Issue 2
Influence of Salinity on Bacterioplankton Communities from the Brazilian Rain Forest to the Coastal Atlantic Ocean
journal, March 2011
- Silveira, Cynthia B.; Vieira, Ricardo P.; Cardoso, Alexander M.
- PLoS ONE, Vol. 6, Issue 3
Metaproteomics of aquatic microbial communities in a deep and stratified estuary
journal, September 2015
- Colatriano, David; Ramachandran, Arthi; Yergeau, Etienne
- PROTEOMICS, Vol. 15, Issue 20
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
journal, February 2016
- Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae
- Journal of Molecular Biology, Vol. 428, Issue 4
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
journal, May 2000
- Yang, Ziheng; Nielsen, Rasmus; Goldman, Nick
- Genetics, Vol. 155, Issue 1
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journal, April 2014
- Kettles, Nicola Louise; Kopriva, Stanislav; Malin, Gill
- PLoS ONE, Vol. 9, Issue 4
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journal, November 2019
- Shen, Mengyuan; Li, Qi; Ren, Minglei
- Frontiers in Microbiology, Vol. 10
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journal, May 2019
- Ren, Ze; Qu, Xiaodong; Peng, Wenqi
- Water, Vol. 11, Issue 5
A novel real-world ecotoxicological dataset of pelagic microbial community responses to wastewater
journal, May 2020
- Ruprecht, J. E.; Glamore, W. C.; Dafforn, K. A.
- Scientific Data, Vol. 7, Issue 1
Patterns and processes of free‐living and particle‐associated bacterioplankton and archaeaplankton communities in a subtropical river‐bay system in South China
journal, January 2020
- Wang, Yongming; Pan, Jie; Yang, Jun
- Limnology and Oceanography, Vol. 65, Issue S1
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