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Shannon diversity index data based on Community Level Physiological Profiling (CLPP) of soil samples from 120 point locations within limestone cedar glades at Stones River National Battlefield near Murfreesboro, Tennessee

Metadata Updated: October 29, 2023

This dataset contains data collected within limestone cedar glades at Stones River National Battlefield (STRI) near Murfreesboro, Tennessee. This dataset contains information on soil microbial metabolic diversity for soil samples obtained from certain quadrat locations (points) within 12 selected cedar glades. This information derives from substrate utilization profiles based on Biolog EcoPlates (Biolog, Inc., Hayward, CA, USA) which were inoculated with soil slurries containing the entire microbial community present in each soil sample. EcoPlates contain 31 sole-carbon substrates (present in triplicate on each plate) and one blank (control) well. Once the microbial community from a soil sample is inoculated onto the plates, the plates are incubated and absorbance readings are taken at intervals.For each quadrat location (point), one soil sample was obtained under sterile conditions, using a trowel wiped with methanol and rinsed with distilled water, and was placed into an autoclaved jar with a tight-fitting lid and placed on ice. Soil samples were transported to lab facilities on ice and immediately refrigerated. Within 24 hours after being removed from the field, soil samples were processed for community level physiological profiling (CLPP) using Biolog EcoPlates. First, for each soil sample three measurements were taken of gravimetric soil water content using a Mettler Toledo HB43 halogen moisture analyzer (Mettler Toledo, Columbus, OH, USA) and the mean of these three SWC measurements was used to calculate the 10-gram dry weight equivalent (DWE) for each soil sample. For each soil sample, a 10-gram DWE of fresh soil was added to 90 milliliters of sterile buffer solution in a 125-milliliter plastic bottle to make the first dilution. Bottles were agitated on a wrist-action shaker for 20 minutes, and a 10-milliliter aliquot was taken from each sample using sterilized pipette tips and added to 90 milliliters of sterile buffer solution to make the second dilution. The bottle containing the second dilution for each sample was agitated for 10 seconds by hand, poured into a sterile tray, and the second dilution was inoculated directly onto Biolog EcoPlates using a sterilized pipette set to deliver 150 microliters into each well. Each plate was immediately covered, placed in a covered box and incubated in the dark at 25 degrees Celcius. Catabolism of each carbon substrate produced a proportional color change response (from the color of the inoculant to dark purple) due to the activity of the redox dye tetrazolium violot (present in all wells including blanks). Plates were read at intervals of 24 hours, 48 hours, 72 hours, 96 hours and 120 hours after inoculation using a Biolog MicroStation plate reader (Biolog, Inc., Hayward, CA, USA) reading absorbance at 590 nanometers.For each soil sample and at each incubation time point, raw absorbance values were transformed according to the equations:T = (C-R) / AWCD; and AWCD = [Σ (C – R)] / nwhere T represents transformed substrate-level response values, C is the absorbance value of control wells (mean of 3 controls), R is the mean absorbance of the response wells (3 wells per carbon substrate), AWCD is average well color development for the plate, and n is the number of carbon substrates (31 for EcoPlates). To integrate time-series data from multiple EcoPlate readings (both for AWCD and also for individual substrates, T), the area under the incubation curve, from 48 hours to 120 hours of incubation time, was calculated.To assess community-level microbial diversity, the Shannon-Weaver index (H) was calculated as follows:H = - ∑ p(ln p)where p is the ratio of the activity of each substrate (T values, area under the incubation curve) to the sum of the activities of all substrates for a given EcoPlate. Thus, the numeric values contained in the fields of this dataset represent H values (Shannon-Weaver index of diversity) based on substrate-utilization diversity of the entire microbial community of each soil sample. Higher values indicate that the entire microbial community metabolized a greater diversity of substrates present on the EcoPlates during the incubation period under consideration. Detailed descriptions of experimental design, field data collection procedures, laboratory procedures, and data analysis are presented in Cartwright (2014).References:Cartwright, J. (2014). Soil ecology of a rock outcrop ecosystem: abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades. Ph.D. dissertation, Tennessee State UniversityCofer, M., Walck, J., and Hidayati, S. (2008). Species richness and exotic species invasion in Middle Tennessee cedar glades in relation to abiotic and biotic factors. The Journal of the Torrey Botanical Society, 135(4), 540–553.Garland, J., & Mills, A. (1991). Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Applied and environmental microbiology, 57(8), 2351–2359.Garland, J. (1997). Analysis and interpretation of community‐level physiological profiles in microbial ecology. FEMS Microbiology Ecology, 24, 289–300.Hackett, C. A., & Griffiths, B. S. (1997). Statistical analysis of the time-course of Biolog substrate utilization. Journal of Microbiological Methods, 30(1), 63–69.Insam, H. (1997). A new set of substrates proposed for community characterization in environmental samples. In H. Insam & A. Rangger (Eds.), Microbial Communities: Functional versus Structural Approaches(pp. 259–260). New York: Springer.Preston-Mafham, J., Boddy, L., & Randerson, P. F. (2002). Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique. FEMS microbiology ecology, 42(1), 1–14. doi:10.1111/j.1574-6941.2002.tb00990.x

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Public: This dataset is intended for public access and use. License: No license information was provided. If this work was prepared by an officer or employee of the United States government as part of that person's official duties it is considered a U.S. Government Work.

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Dates

Metadata Created Date June 1, 2023
Metadata Updated Date October 29, 2023

Metadata Source

Harvested from DOI EDI

Additional Metadata

Resource Type Dataset
Metadata Created Date June 1, 2023
Metadata Updated Date October 29, 2023
Publisher U.S. Geological Survey
Maintainer
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Identifier USGS:55afce3ce4b09a3b01b51e52
Data Last Modified 20200821
Category geospatial
Public Access Level public
Bureau Code 010:12
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Metadata Catalog ID https://datainventory.doi.gov/data.json
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
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Harvest Source Id 52bfcc16-6e15-478f-809a-b1bc76f1aeda
Harvest Source Title DOI EDI
Metadata Type geospatial
Old Spatial -86.438456,35.87077,-86.433152,35.874081
Publisher Hierarchy White House > U.S. Department of the Interior > U.S. Geological Survey
Source Datajson Identifier True
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Source Schema Version 1.1
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