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Harvard Forest Data Archive

HF304

Effects of Warming on Soil Microbial Oxidative Activity at Harvard Forest 2013

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Data

Overview

  • Lead: Kristen DeAngelis, Jerry Melillo, Grace Pold
  • Investigators:
  • Contact: Information Manager
  • Start date: 2013
  • End date: 2013
  • Status: complete
  • Location: Prospect Hill Tract (Harvard Forest)
  • Latitude: +42.54 degrees
  • Longitude: -72.18 degrees
  • Elevation: 365 meter
  • Datum: WGS84
  • Taxa:
  • Release date: 2023
  • Language: English
  • EML file: knb-lter-hfr.304.4
  • DOI: digital object identifier
  • EDI: data package
  • DataONE: data package
  • Related links:
  • Study type: short-term measurement
  • Research topic: large experiments and permanent plot studies; physiological ecology, population dynamics and species interactions; soil carbon and nitrogen dynamics
  • LTER core area: population studies, organic matter movement
  • Keywords: climate change, community dynamics, decomposition, microbes, soil warming
  • Abstract:

    As Earth’s climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community’s capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.

  • Methods:

    A full description of the methods is found in the published manuscript. Briefly, to each of four replicate heated and four replicate disturbance control plots, we horizontally deployed separate pouches containing lignin-amended (Sigma no. 471003) or unamended Bio-Sep bead (Microbial Insights, Knoxville TN) pouches (details in next section). Pouches were deployed as either “surface” bags, or as “subsurface” bags. Surface bags were placed on the surface of the soil under the leaf litter layer. Subsurface bead bags were buried in the soil between the organic horizon and the mineral soil. Bags were deployed for 11 weeks, after which amended and unamended beads were assayed for oxidative enzyme activity (with activities measured on a per gram bead basis as well as a per cell basis), as well as community composition by sequencing. The sequences were then quantitatively compared to known lignin-degrading species. Sequence data available under BioProject ID PRJNA242968.

  • Organization: Harvard Forest. 324 North Main Street, Petersham, MA 01366, USA. Phone (978) 724-3302. Fax (978) 724-3595.

  • Project: The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. (ROR).

  • Funding: National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210.

  • Use: This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

  • License: Creative Commons Zero v1.0 Universal (CC0-1.0)

  • Citation: DeAngelis K, Melillo J, Pold G. 2023. Effects of Warming on Soil Microbial Oxidative Activity at Harvard Forest 2013. Harvard Forest Data Archive: HF304 (v.4). Environmental Data Initiative: https://doi.org/10.6073/pasta/c9649f14260def9e9a540979983fd6e4.

Detailed Metadata

hf304-01: biosep oxidative summary

  1. bag: bag identification number
  2. horizon: location of bag deployment
    • subsurface: bags incubated between organic horizon and mineral soil
    • surface: bags deployed on surface of organic horizon below litter layer
  3. amendment: whether or not beads were amended with lignin
    • Unamended: not amended
    • Lignin: amended
  4. plot: plot ID for deployment in long-term warming plots
  5. treatment: plot warming treatment
    • Heated: 5C heated treatment
    • Control: disturbance control plots
  6. bag.id: bag identification number
  7. bead.wt: mass of beads used in assay slurry in 40 ml buffer (unit: gram / missing value: NA)
  8. po: phenol oxidase activity as change in A460nm of 50ul enzyme assay supernatant over the first three hours of the assay (ie it is a slope), assuming the initial absorbance was zero (unit: number / missing value: NA)
  9. hpo: peroxidase activity calculated using the change in A460nm of 50ul enzyme assay supernatant over the first three hours of the assay (ie it is a slope), assuming the initial absorbance was zero. The greatest changes occurred in the first 20 minutes, however these these initial values cannot be used due to the large variablity in blanks. (unit: number / missing value: NA)
  10. net.hpo: net peroxidase activity, calculated as plates with H2O2 minus plates without (unit: number / missing value: NA)
  11. po.activity: calculated using the formula Activity = (slope)*volume of buffer used (40ml)/(extinction coefficient (7.9umol)* volume plated (0.05ml)*g beads), where slope is the phenol oxidase slope (unit: micromolePerGramPerHour / missing value: NA)
  12. oxi.beads: activity = (slope)*volume of buffer used (40ml)/(extinction coefficient (7.9umol)* volume plated (0.05ml)*g beads), using the peroxidase (ie +H2O2 wells) slope (unit: gram / missing value: NA)
  13. net.peroxidase: difference between OXI.beads and PO activity, since phenol oxidases are active under the addition of H2O2, along with other activities (unit: micromolePerGram / missing value: NA)
  14. cells.bead: direct counts of cells detected per gram bead (unit: number / missing value: NA)
  15. po.sa: phenol oxidase specific activity (substrate converted per hour per 1e9 cells) (unit: dimensionless / missing value: NA)
  16. oxi.cells: total oxidative specific activity (substrate converted per hour per 1e9 cells) (unit: dimensionless / missing value: NA)
  17. net.perox: net phenol oxidase specific activity (substrate converted per hour per 1e9 cells) (unit: dimensionless / missing value: NA)