Dataset Listing

Bisley - Soil Microbes, Soil Biogeochemistry - Iron redox, Soil Microbiome (2012-2017)

Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome

Variables:  ferric ion, ferrous ion, Biomass, soil bacterial DNA,

Standard Variables:  Biomass|Biomass, soil bacterial deoxyribonucleic acid (DNA)

Date Range:  (2012-2017)

Dataset Creators/Authors:  Wilmoth, Jared Lee ; Moran, Mary Ann; Thompson, Aaron

Contact:  Miguel Leon,

Field Area:   Bisley

Keywords & XML
  • Description


    Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O2).


    We repeatedly exposed anoxic (4% H2:96% N2) suspensions of soil from the Luquillo Critical Zone Observatory to 1.05 × 102, 1.05 × 103, and 1.05 × 104 mmol O2 kg−1 soil h−1 during pulsed oxygenation treatments. Metatranscriptomic analysis and 57Fe Mössbauer spectroscopy were used to investigate changes in Fe(III)-reducer gene expression and Fe(III) crystallinity, respectively.


    Slow oxygenation resulted in soil Fe-(oxyhydr)oxides of higher crystallinity (38.1 ± 1.1% of total Fe) compared to fast oxygenation (30.6 ± 1.5%, P < 0.001). Transcripts binning to the genomes of Fe(III)-reducers Anaeromyxobacter, Geobacter, and Pelosinus indicated significant differences in extracellular electron transport (e.g., multiheme cytochrome c, multicopper oxidase, and type-IV pilin gene expression), adhesion/contact (e.g., S-layer, adhesin, and flagellin gene expression), and selective microbial competition (e.g., bacteriocin gene expression) between the slow and fast oxygenation treatments during microbial Fe(III) reduction. These data also suggest that diverse Fe(III)-reducer functions, including cytochrome-dependent extracellular electron transport, are associated with type-III fibronectin domains. Additionally, the metatranscriptomic data indicate that Methanobacterium was significantly more active in the reduction of CO2 to CH4 and in the expression of class(III) signal peptide/type-IV pilin genes following repeated fast oxygenation compared to slow oxygenation.


    This study demonstrates that specific Fe(III)-reduction mechanisms in mixed Fe(III)-reducer populations are uniquely sensitive to the rate of O2 influx, likely mediated by shifts in soil Fe(III)-(oxyhydr)oxide crystallinity. Overall, we provide evidence that transient oxygenation events play an important role in directing anaerobic pathways within soil microbiomes, which is expected to alter Fe and C cycling in redox-dynamic environments.
  • Keywords

    Soil microbiome, redox cycling, microbial FE(III) reduction, carbon cyling, metatranscriptomics, mössbauer spectroscopy

    XML Metadata

    XML is in ISO-19115 geographic metadata format, compatible with ESRI Geoportal Server.

  • Citation for This Dataset

    Jared Lee Wilmoth, Mary Ann Moran, Aaron Thompson (2018): Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome. Microbiome. DOI: 10.1186/s40168-018-0574-5

    Citation for This Webpage

    Wilmoth, Jared Lee ; Moran, Mary Ann; Thompson, Aaron (2017). "CZO Dataset: Bisley - Soil Microbes, Soil Biogeochemistry (2012-2017) - Iron redox, Soil Microbiome." Retrieved 16 Feb 2020, from

  • Publications

    Primary Publications


    Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome. Jared Lee Wilmoth, Mary Ann Moran, Aaron Thompson (2018): Microbiome


Bisley - Soil metagenome

(3306)   Data Level 0

Data Use Policy
Data Sharing Policy
  • Data Use Policy

    DRAFT v.0.4.0

    1. Use our data freely. All CZO Data Products* except those labelled Private** are released to the public and may be freely copied, distributed, edited, remixed, and built upon under the condition that you give acknowledgement as described below. Non-CZO data products — like those produced by USGS or NOAA — have their own use policies, which should be followed.

    2. Give proper citation and acknowledgement. Publications, models and data products that make use of these datasets must include proper citation and acknowledgement. Most importantly, provide a citation in a similar way as a journal article (i.e. author, title, year of publication, name of CZO “publisher”, edition or version, and URL or DOI access information. See Also include at least a brief acknowledgement such as: “Data were provided by the NSF-supported Southern Sierra Critical Zone Observatory” (replace with the appropriate observatory name).

    3. Let us know how you will use the data. The dataset creators would appreciate hearing of any plans to use the dataset. Consider consultation or collaboration with dataset creators.

    *CZO Data Products.  Defined as a data collected with any monetary or logistical support from a CZO.

    **Private. Most private data will be released to the public within 1-2 years, with some exceptionally challenging datasets up to 4 years. To inquire about potential earlier use, please contact us.

  • Data Sharing Policy

    DRAFT v.0.2.5

    All CZO investigators and collaborators who receive material or logistical support from a CZO agree to:

    1. Share data privately within 1 year. CZO investigators and collaborators agree to provide CZO Data Products* — including data files and metadata for raw, quality controlled and/or derived data — to CZO data managers within one year of collection of samples, in situ or experimental data. By default, data values will be held in a Private CZO Repository**, but metadata will be made public and will provide full attribution to the Dataset Creators†.

    2. Release data to public within 2 years. CZO Dataset Creators will be encouraged after one year to release data for public access. Dataset Creators may chose to publish or release data sooner.

    3. Request, in writing, data privacy up to 4 years. CZO PIs will review short written applications to extend data privacy beyond 2 years and up to 4 years from time of collection. Extensions beyond 3 years should not be the norm, and will be granted only for compelling cases.

    4. Consult with creators of private CZO datasets prior to use. In order to enable the collaborative vision of the CZO program, data in private CZO repositories will be available to other investigators and collaborators within that CZO. Releasing or publishing any derivative of such private data without explicit consent from the dataset creators will be considered a serious scientific ethics violation.

    * CZO Data Products. Defined as data collected with any monetary or logistical support from a CZO. Logistical support includes the use of any CZO sensors, sampling infrastructure, equipment, vehicles, or labor from a supported investigator, student or staff person. CZO Data Products can acknowledge multiple additional sources of support.

    ** Private CZO Repository. Defined as a password-protected directory on each CZO’s data server. Files will be accessible by all investigators and collaborators within the given CZO and logins will be maintained by that local CZO’s data managers. Although data values will not be accessible by the public or ingested into any central data system (i.e. CUAHSI HIS), metadata will be fully discoverable by the public. This provides the dual benefit of giving attribution and credit to dataset creators and the CZO in general, while maintaining protection of intellectual property while publications are pending.

    † Dataset Creators. Defined as the people who are responsible for designing, collecting, analyzing and providing quality assurance for a dataset. The creators of a dataset are analogous to the authors of a publication, and datasets should be cited in an analogous manner following the emerging international guidelines described at

CZO Field Areas


CZO Authors

Explore Further

data |

Explore Further