Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Omics Data Sets

Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)

Ariane L. Peralta, Regina B. Bledsoe, Mario E. Muscarella, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishnaveni Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I-Min A. Chen, Natalia N. Ivanova, Nikos C. Kyrpides, Tijana Glavina del Rio, Emiley A. Eloe-Fadrosh
J. Cameron Thrash, Editor
Ariane L. Peralta
aDepartment of Biology, East Carolina University, Howell Science Complex, Greenville, North Carolina, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ariane L. Peralta
Regina B. Bledsoe
aDepartment of Biology, East Carolina University, Howell Science Complex, Greenville, North Carolina, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mario E. Muscarella
bInstitute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mario E. Muscarella
Marcel Huntemann
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alicia Clum
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brian Foster
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Bryce Foster
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simon Roux
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Krishnaveni Palaniappan
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Neha Varghese
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Supratim Mukherjee
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
T. B. K. Reddy
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for T. B. K. Reddy
Chris Daum
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alex Copeland
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
I-Min A. Chen
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Natalia N. Ivanova
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nikos C. Kyrpides
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tijana Glavina del Rio
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Emiley A. Eloe-Fadrosh
cJoint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. Cameron Thrash
University of Southern California
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00882-20
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and plant presence. These wetland soil metagenomes will deepen our understanding of how hydrology and vegetation influence microbial functional diversity.

ANNOUNCEMENT

Microbial community structure, soil physicochemical properties, and the abundance and composition of vegetation interact to influence biogeochemical functions (1). Changes in wetland hydrology due to drought, draining, and rewetting cause shifts in soil redox potential, microbial community composition, and associated ecosystem processes such as greenhouse gas (GHG) production (2–6). Vegetation also affects microbial processes by facilitating the transport of oxygen into the root zone and the transport of methane from the root zone into the atmosphere (7, 8). Here, we present wetland soil metagenomes from a mesocosm experiment in which we manipulated hydrology and plant presence to examine microbial community responses. These data complement targeted amplicon sequencing data, GHG fluxes, and soil physicochemical properties from the wetland mesocosm experiment (9).

We collected wetland soils from a restored coastal freshwater wetland at the Timberlake Observatory for Wetland Restoration on the Albemarle Peninsula in Tyrell County, North Carolina (latitude, 35.8959; longitude, −76.1658). We collected soils from three locations with different water table levels (−20 cm, −10 cm, and 0 cm) (10). We altered redox conditions by manipulating hydrology over 8 weeks. The experimental design and sampling details were published by Bledsoe and Peralta (9). We collected and combined six soil cores (3-cm diameter, 10-cm depth) from plant or no-plant areas. We completed 16S rRNA amplicon sequencing (NCBI BioProject PRJNA636184), GHG flux measurements, and soil environmental analyses (9). We sequenced metagenomes that represented the most distinct microbial communities based on amplicon sequencing, and we chose the following samples: wetland soils sampled from field sites at which the water table measured −20 cm and 0 cm, to capture “mesocosm baseline” (n = 8) functional diversity, and a subset of samples at the end of the 8-week hydrologic manipulation (i.e., prolonged drying or wetting only) in the presence or absence of vegetation (n = 16) (9).

We used the Qiagen DNeasy PowerMax soil kit to extract genomic DNA from freeze-dried soils. Purified DNA products were sent to the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) for sequencing and analysis. Metagenomes were sequenced at the DOE JGI (GitHub [see SupplementalTableS1_MetagenomeSummary_Peralta_et_al.csv at https://doi.org/10.5281/zenodo.4042110]), and project information can be accessed under GOLD (11) study project accession number Gs0142547 and NCBI BioProject accession number PRJNA641216. Plate-based DNA library preparation for Illumina sequencing was performed according to published protocols in GitHub (see Supplemental_Methods_Details_MRA_WetlandSoilMetagenomes.txt at https://doi.org/10.5281/zenodo.4042110). The sequencing project resulted in 583.2 Gbp of raw sequence data. The average read length for each metagenome is found in GitHub (see SupplementalTableS1_MetagenomeSummary_Peralta_et_al.csv at https://doi.org/10.5281/zenodo.4042110). These data were processed using the DOE JGI Metagenome Annotation Pipeline using IMG/M v.5.0.9 (12–14). Initial sequence quality control details can be found in GitHub (see Supplemental_Methods_Details_MRA_WetlandSoilMetagenomes.txt at https://doi.org/10.5281/zenodo.4042110). Illumina reads were quality control filtered according to the protocol described in GitHub (see Supplemental_Methods_Details_MRA_WetlandSoilMetagenomes.txt at https://doi.org/10.5281/zenodo.4042110).

Annotation and gene calling resulted in 600,507 ± 172,049 annotated contigs per sample (mean ± standard deviation [SD]), with a mean of 998,604 gene features (SD, 307,431 gene features) identified in each (Table 1). Based on phylogenetic associations (determined on the basis of bidirectional best hits to genes in other genomes), the estimated alpha diversity across all metagenomes is 10,365 ± 837 operational taxonomic units (OTUs) (mean ± SD) (GitHub [see SupplementalTableS1_MetagenomeSummary_Peralta_et_al.csv at https://doi.org/10.5281/zenodo.4042110]).

View this table:
  • View inline
  • View popup
  • Download powerpoint
TABLE 1

Annotation and gene-calling summary for the 24 metagenomes

Data availability.Metagenomes were sequenced at the DOE JGI, and the study information can be found under GOLD study project accession number Gs0142547 and NCBI BioProject accession number PRJNA641216. Additional sample-specific metagenome statistics can be found in GitHub (see SupplementalTableS1_MetagenomeSummary_Peralta_et_al.csv at https://doi.org/10.5281/zenodo.4042110). Details on metagenomic library preparation and sequence filtering can be found in GitHub (see Supplemental_Methods_Details_MRA_WetlandSoilMetagenomes.txt at https://doi.org/10.5281/zenodo.4042110).

ACKNOWLEDGMENTS

We thank J. LeCrone, L. Armstrong, M. Stillwagon, G. Gunderson, C. Eakins, J. Basco, and C. Bledsoe for field and laboratory assistance. We thank J. Gill and the East Carolina University grounds crew for their efforts in maintaining the grounds surrounding the shade house.

This work was supported by the National Science Foundation (Graduate Research Fellowship Program [GRFP] grant to R.B.B. and grant DEB 1845845 to A.L.P.). The metagenomes were produced by the DOE JGI under the Community Science Program (CSP) (JGI CSP grant 503952). The work conducted by the DOE JGI, a DOE Office of Science User Facility, is supported under contract DE-AC02-05CH11231.

FOOTNOTES

    • Received 29 July 2020.
    • Accepted 15 September 2020.
    • Published 8 October 2020.
  • Copyright © 2020 Peralta et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Jansson JK,
    2. Hofmockel KS
    . 2020. Soil microbiomes and climate change. 1. Nat Rev Microbiol 18:35–46. doi:10.1038/s41579-019-0265-7.
    OpenUrlCrossRef
  2. 2.↵
    1. Peralta AL,
    2. Ludmer S,
    3. Matthews JW,
    4. Kent AD
    . 2014. Bacterial community response to changes in soil redox potential along a moisture gradient in restored wetlands. Ecol Eng 73:246–253. doi:10.1016/j.ecoleng.2014.09.047.
    OpenUrlCrossRef
  3. 3.↵
    1. Lazcano C,
    2. Deol AS,
    3. Brummell ME,
    4. Strack M
    . 2020. Interactive effects of vegetation and water table depth on belowground C and N mobilization and greenhouse gas emissions in a restored peatland. Plant Soil 448:299–313. doi:10.1007/s11104-020-04434-2.
    OpenUrlCrossRef
  4. 4.↵
    1. Bansal S,
    2. Johnson OF,
    3. Meier J,
    4. Zhu X
    . 2020. Vegetation affects timing and location of wetland methane emissions. J Geophys Res Biogeosci 125:e2020JG005777.
  5. 5.↵
    1. Ou Y,
    2. Rousseau AN,
    3. Wang L,
    4. Yan B,
    5. Gumiere T,
    6. Zhu H
    . 2019. Identification of the alteration of riparian wetland on soil properties, enzyme activities and microbial communities following extreme flooding. Geoderma 337:825–833. doi:10.1016/j.geoderma.2018.10.032.
    OpenUrlCrossRef
  6. 6.↵
    1. Peralta AL,
    2. Ludmer S,
    3. Kent AD
    . 2013. Hydrologic history influences microbial community composition and nitrogen cycling under experimental drying/wetting treatments. Soil Biol Biochem 66:29–37. doi:10.1016/j.soilbio.2013.06.019.
    OpenUrlCrossRefWeb of Science
  7. 7.↵
    1. Chanton JP
    . 2005. The effect of gas transport on the isotope signature of methane in wetlands. Org Geochem 36:753–768. doi:10.1016/j.orggeochem.2004.10.007.
    OpenUrlCrossRefWeb of Science
  8. 8.↵
    1. Carmichael MJ,
    2. Bernhardt ES,
    3. Bräuer SL,
    4. Smith WK
    . 2014. The role of vegetation in methane flux to the atmosphere: should vegetation be included as a distinct category in the global methane budget? Biogeochemistry 119:1–24. doi:10.1007/s10533-014-9974-1.
    OpenUrlCrossRef
  9. 9.↵
    1. Bledsoe RB,
    2. Peralta AL
    . 2020. Dynamic hydrology and plant-mediated effects reduce greenhouse gas emissions and alter wetland microbial communities. bioRxiv doi:10.1101/2020.06.29.178533.
    OpenUrlCrossRef
  10. 10.↵
    1. Ardón M,
    2. Morse JL,
    3. Doyle MW,
    4. Bernhardt ES
    . 2010. The water quality consequences of restoring wetland hydrology to a large agricultural watershed in the southeastern coastal plain. Ecosystems 13:1060–1078. doi:10.1007/s10021-010-9374-x.
    OpenUrlCrossRef
  11. 11.↵
    1. Mukherjee S,
    2. Stamatis D,
    3. Bertsch J,
    4. Ovchinnikova G,
    5. Katta HY,
    6. Mojica A,
    7. Chen I-MA,
    8. Kyrpides NC,
    9. Reddy TBK
    . 2019. Genomes Online Database (GOLD) v.7: updates and new features. Nucleic Acids Res 47:D649–D659. doi:10.1093/nar/gky977.
    OpenUrlCrossRef
  12. 12.↵
    1. Markowitz VM,
    2. Chen I-MA,
    3. Chu K,
    4. Szeto E,
    5. Palaniappan K,
    6. Pillay M,
    7. Ratner A,
    8. Huang J,
    9. Pagani I,
    10. Tringe S,
    11. Huntemann M,
    12. Billis K,
    13. Varghese N,
    14. Tennessen K,
    15. Mavromatis K,
    16. Pati A,
    17. Ivanova NN,
    18. Kyrpides NC
    . 2014. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res 42:D568–D573. doi:10.1093/nar/gkt919.
    OpenUrlCrossRefPubMedWeb of Science
  13. 13.↵
    1. Huntemann M,
    2. Ivanova NN,
    3. Mavromatis K,
    4. Tripp HJ,
    5. Paez-Espino D,
    6. Tennessen K,
    7. Palaniappan K,
    8. Szeto E,
    9. Pillay M,
    10. Chen I-MA,
    11. Pati A,
    12. Nielsen T,
    13. Markowitz VM,
    14. Kyrpides NC
    . 2016. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand Genomic Sci 11:17. doi:10.1186/s40793-016-0138-x.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Chen I-MA,
    2. Markowitz VM,
    3. Chu K,
    4. Palaniappan K,
    5. Szeto E,
    6. Pillay M,
    7. Ratner A,
    8. Huang J,
    9. Andersen E,
    10. Huntemann M,
    11. Varghese N,
    12. Hadjithomas M,
    13. Tennessen K,
    14. Nielsen T,
    15. Ivanova NN,
    16. Kyrpides NC
    . 2017. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 45:D507–D516. doi:10.1093/nar/gkw929.
    OpenUrlCrossRefPubMed
PreviousNext
Back to top
Download PDF
Citation Tools
Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)
Ariane L. Peralta, Regina B. Bledsoe, Mario E. Muscarella, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishnaveni Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I-Min A. Chen, Natalia N. Ivanova, Nikos C. Kyrpides, Tijana Glavina del Rio, Emiley A. Eloe-Fadrosh
Microbiology Resource Announcements Oct 2020, 9 (41) e00882-20; DOI: 10.1128/MRA.00882-20

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)
Ariane L. Peralta, Regina B. Bledsoe, Mario E. Muscarella, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishnaveni Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I-Min A. Chen, Natalia N. Ivanova, Nikos C. Kyrpides, Tijana Glavina del Rio, Emiley A. Eloe-Fadrosh
Microbiology Resource Announcements Oct 2020, 9 (41) e00882-20; DOI: 10.1128/MRA.00882-20
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X