Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

Abraham, Briana S.; Caglayan, Deniz; Carrillo, Natalie V.; Chapman, Matthew C.; Hagan, Claire T.; Hansen, Skye T.; Jeanty, Ralph O.; Klimczak, Alexander A.; Klingler, Marcos J.; Kutcher, Thomas P.; Levy, Sydney H.; Millard-Bruzos, Angel A.; Moore, Thomas B.; Prentice, David J.; Prescott, Matthew E.; Roehm, Richard; Rose, Jordan A.; Yin, Mulan; Hyodo, Ayumi; Lail, Kathleen; Daum, Christopher; Clum, Alicia; Copeland, Alex; Seshadri, Rekha; del Rio, Tijana Glavina; Eloe-Fadrosh, Emiley A.; Benskin, Jonathan B.

doi:10.1186/s40793-019-0352-4

Title: Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

Journal Article · 20 January 2020 · Environmental Microbiome

DOI: https://doi.org/10.1186/s40793-019-0352-4 · OSTI ID:1618974

Abraham, Briana S.; Caglayan, Deniz; Carrillo, Natalie V.; Chapman, Matthew C.; Hagan, Claire T.; Hansen, Skye T.; Jeanty, Ralph O.; Klimczak, Alexander A.; Klingler, Marcos J.; Kutcher, Thomas P.; Levy, Sydney H.; Millard-Bruzos, Angel A.; Moore, Thomas B.; Prentice, David J.; Prescott, Matthew E.; Roehm, Richard; Rose, Jordan A.; Yin, Mulan; Hyodo, Ayumi; Lail, Kathleen more »

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618974

Journal Information:: Environmental Microbiome, Journal Name: Environmental Microbiome Journal Issue: 1 Vol. 15; ISSN 2524-6372

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (17)

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DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria Geets, Joke; Borremans, Brigitte; Diels, Ludo Journal of Microbiological Methods, Vol. 66, Issue 2 https://doi.org/10.1016/j.mimet.2005.11.002	journal	August 2006
The abundance of nitrogen cycle genes amoA and nifH depends on land-uses and soil types in South-Eastern Australia Hayden, Helen L.; Drake, Judy; Imhof, Mark Soil Biology and Biochemistry, Vol. 42, Issue 10 https://doi.org/10.1016/j.soilbio.2010.06.015	journal	October 2010
Shotgun metagenomics, from sampling to analysis Quince, Christopher; Walker, Alan W.; Simpson, Jared T. Nature Biotechnology, Vol. 35, Issue 9 https://doi.org/10.1038/nbt.3935	journal	September 2017
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes Delmont, Tom O.; Quince, Christopher; Shaiber, Alon Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0176-9	journal	June 2018
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
Genomes OnLine database (GOLD) v.7: updates and new features Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky977	journal	October 2018
Actinobacteria within soils: capacities for mutualism, symbiosis and pathogenesis Schrempf, Hilde FEMS Microbiology Letters, Vol. 342, Issue 2 https://doi.org/10.1111/1574-6968.12147	journal	April 2013
Distribution, Activities, and Interactions of Methanogens and Sulfate-Reducing Prokaryotes in the Florida Everglades Bae, Hee-Sung; Holmes, M. Elizabeth; Chanton, Jeffrey P. Applied and Environmental Microbiology, Vol. 81, Issue 21 https://doi.org/10.1128/AEM.01583-15	journal	August 2015
Methanogens Are Major Contributors to Nitrogen Fixation in Soils of the Florida Everglades Bae, Hee-Sung; Morrison, Elise; Chanton, Jeffrey P. Applied and Environmental Microbiology, Vol. 84, Issue 7 https://doi.org/10.1128/AEM.02222-17	journal	January 2018
Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities Hester, Eric R.; Harpenslager, Sarah F.; van Diggelen, Josepha M. H. mSystems, Vol. 3, Issue 1 https://doi.org/10.1128/mSystems.00214-17	journal	January 2018
Microbial diversity and soil physiochemical characteristic of higher altitude Kumar, Saurabh; Suyal, Deep Chandra; Yadav, Amit PLOS ONE, Vol. 14, Issue 3 https://doi.org/10.1371/journal.pone.0213844	journal	March 2019
Sulfate-reducing microorganisms in wetlands – fameless actors in carbon cycling and climate change Pester, Michael Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00072	journal	January 2012
Microbiology of wetlands Bodelier, Paul L. E.; Dedysh, Svetlana N. Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00079	journal	January 2013
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59 BASIC BIOLOGICAL SCIENCES
everglades
methane production
nitrogen fixation
prokaryotes
shotgun metagenomics
soil metagenome

Title: Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

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References (17)

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