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

Abstract

Background: Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction). Methods: Shotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen. Results: The three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed themore » presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration. Conclusion: This Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1618974
Alternate Identifier(s):
OSTI ID: 1604726
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Environmental Microbiome
Additional Journal Information:
Journal Name: Environmental Microbiome Journal Volume: 15 Journal Issue: 1; Journal ID: ISSN 2524-6372
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; shotgun metagenomics; methane production; nitrogen fixation; everglades; soil metagenome; prokaryotes

Citation Formats

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., and Benskin, Jonathan B. Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades. United Kingdom: N. p., 2020. Web. https://doi.org/10.1186/s40793-019-0352-4.
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. Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades. United Kingdom. https://doi.org/10.1186/s40793-019-0352-4
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., and Benskin, Jonathan B. Tue . "Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades". United Kingdom. https://doi.org/10.1186/s40793-019-0352-4.
@article{osti_1618974,
title = {Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades},
author = {Abraham, Briana S. and Caglayan, Deniz and Carrillo, Natalie V. and Chapman, Matthew C. and Hagan, Claire T. and Hansen, Skye T. and Jeanty, Ralph O. and Klimczak, Alexander A. and Klingler, Marcos J. and Kutcher, Thomas P. and Levy, Sydney H. and Millard-Bruzos, Angel A. and Moore, Thomas B. and Prentice, David J. and Prescott, Matthew E. and Roehm, Richard and Rose, Jordan A. and Yin, Mulan and Hyodo, Ayumi and Lail, Kathleen and Daum, Christopher and Clum, Alicia and Copeland, Alex and Seshadri, Rekha and del Rio, Tijana Glavina and Eloe-Fadrosh, Emiley A. and Benskin, Jonathan B.},
abstractNote = {Background: Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction). Methods: Shotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen. Results: The three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration. Conclusion: This Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades.},
doi = {10.1186/s40793-019-0352-4},
journal = {Environmental Microbiome},
number = 1,
volume = 15,
place = {United Kingdom},
year = {2020},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
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https://doi.org/10.1186/s40793-019-0352-4

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