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Title: Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities

 [1];  [2];  [3];  [1];  [2];  [2];  [4];  [1]
  1. Oregon State Univ., Corvallis, OR (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  3. Univ. of Washington, Seattle, WA (United States)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1488816
Report Number(s):
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
Frontiers Research Foundation
Country of Publication:
United States
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. doi:
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. doi:
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 = {2018},
month = {6}

Journal Article:
Free Publicly Available Full Text
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Cited by: 6 works
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Figures / Tables:

Table 1. 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 » column, typefaces indicate the following classes: bold = Metabolism; italic = Cell Processing and Signaling; underlined = Information Storage and Processing; normal = Poorly characterized.« less

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Works referenced in this record:

Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries
journal, March 2002

Influence of Salinity on Bacterioplankton Communities from the Brazilian Rain Forest to the Coastal Atlantic Ocean
journal, March 2011

Sipros Ensemble improves database searching and filtering for complex metaproteomics
journal, September 2017

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
  • DOI: 10.1093/nar/gkv1248

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
  • DOI: 10.3391/mbi.2016.7.2.02

Gene and translation initiation site prediction in metagenomic sequences
journal, July 2012

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
  • DOI: 10.1128/AEM.00592-07

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
  • DOI: 10.1038/ismej.2013.104

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
  • DOI: 10.3389/fmicb.2016.00211

Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
journal, January 2005

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
  • DOI: 10.1186/1471-2164-10-639

Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time
journal, March 2004

Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon
journal, March 2010

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
  • DOI: 10.1101/gr.186072.114

Fast and sensitive protein alignment using DIAMOND
journal, November 2014

  • Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3176

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014

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
  • DOI: 10.1038/nature12857

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
  • DOI: 10.1038/nrmicro2259

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
  • DOI: 10.3389/fmicb.2013.00120

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
  • DOI: 10.1093/nar/gkv1344

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
  • DOI: 10.1038/ismej.2010.185

Coupling Between the Coastal Ocean and Yaquina Bay, Oregon: Importance of Oceanic Inputs Relative to Other Nitrogen Sources
journal, January 2009

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
  • DOI: 10.1038/85686

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
  • DOI: 10.1128/AEM.01541-09

Phylogenetically conserved resource partitioning in the coastal microbial loop
journal, August 2017

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
  • DOI: 10.3389/fmicb.2015.01438

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
  • DOI: 10.1038/ismej.2014.67

Attached and Free Bacteria in an Estuary with Abundant Suspended Solids
journal, December 1977

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
  • DOI: 10.1073/pnas.1101405108

Particle-attached bacteria and heterotrophic plankton associated with the Columbia River estuarine turbidity maxima
journal, January 1996

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
  • DOI: 10.1111/brv.12055

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
  • DOI: 10.1111/1365-2745.12585

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
  • DOI: 10.1128/AEM.01299-16

How do divergent ecological strategies emerge among marine bacterioplankton lineages?
journal, September 2015

Oceanography of the U.S. Pacific Northwest Coastal Ocean and estuaries with application to coastal ecology
journal, August 2003

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
journal, January 2015

STAMP: statistical analysis of taxonomic and functional profiles
journal, July 2014

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
journal, February 2012

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
  • DOI: 10.3354/ame014007

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
  • DOI: 10.1021/acs.est.5b02630

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
  • DOI: 10.1128/AEM.02680-13

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
  • DOI: 10.1038/nature03170

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
journal, April 2015

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
  • DOI: 10.1071/MF00084

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
  • DOI: 10.1073/pnas.0801925105

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
  • DOI: 10.1016/j.jmb.2015.11.006

Metagenome-assembled genomes uncover a global brackish microbiome
journal, December 2015

A terrestrial organic matter depocenter on a high-energy margin: The Umpqua River system, Oregon
journal, May 2012

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
journal, June 2013

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015

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
  • DOI: 10.1128/AEM.00395-16

Marine metaproteomics: deciphering the microbial metabolic food web
journal, May 2014

Conservation evaluation and phylogenetic diversity
journal, January 1992

Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem
journal, September 2014

Genetic diversity in Sargasso Sea bacterioplankton
journal, May 1990

  • Giovannoni, Stephen J.; Britschgi, Theresa B.; Moyer, Craig L.
  • Nature, Vol. 345, Issue 6270
  • DOI: 10.1038/345060a0

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
  • DOI: 10.1016/0016-7037(87)90080-9

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
  • DOI: 10.1093/nar/gkw290

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
  • DOI: 10.1128/MMBR.00037-15

Metagenomic biomarker discovery and explanation
journal, January 2011

Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro
journal, August 2004

Marine Microbes See a Sea of Gradients
journal, November 2012

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing
journal, August 2014

Phylogenetic limiting similarity and competitive exclusion: Phylogenetic relatedness and competition
journal, June 2011

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
  • DOI: 10.1093/nar/gkv1145

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
  • DOI: 10.1002/lno.10601

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
  • DOI: 10.1016/j.chom.2015.01.011

Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
journal, February 2014

A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence
journal, April 2010

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
  • DOI: 10.4319/lo.2002.47.2.0343

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
  • DOI: 10.1093/femsec/fiw133

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
  • DOI: 10.1038/msb.2011.75

Evidence for positive selection on the E2 gene of bovine viral diarrhoea virus type 1
journal, June 2007

Bacterial Biogeography across the Amazon River-Ocean Continuum
journal, May 2017

Particulate organic carbon in the estuarine turbidity maxima of the Gironde, Loire and Seine estuaries: origin and lability
journal, September 2007

Bacterial sulfate reduction within reduced microniches of oxidized marine sediments
journal, January 1977

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
  • DOI: 10.1016/j.ecss.2010.07.012

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
  • DOI: 10.1038/ismej.2014.254

Proteinortho: Detection of (Co-)orthologs in large-scale analysis
journal, April 2011

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
  • DOI: 10.1002/jgrg.20024

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
  • DOI: 10.1073/pnas.241370698

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
  • DOI: 10.1186/1471-2148-8-313

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
  • DOI: 10.1038/ismej.2017.26

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
  • DOI: 10.1002/pmic.201500079

Phylogenetic Analysis of Particle-Attached and Free-Living Bacterial Communities in the Columbia River, Its Estuary, and the Adjacent Coastal Ocean
journal, July 1999

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