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Scale dependence in functional equivalence and difference in the soil microbiome

Cite this dataset

Polussa, Alexander (2022). Scale dependence in functional equivalence and difference in the soil microbiome [Dataset]. Dryad.


Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. A similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Our findings confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extends this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes can generate microbial functional legacies.


Full methods can be found in the associated manuscript.

Briefly, twenty-seven 1 m2 plots within each of two forest sites (SCBI: Smithsonian Conservation Biological Institute, Front Royal, VA and HARV: Harvard Forest, Petersham, MA) were set up in fall 2019. Soil measurements (temperature, moisture, pH, etc) were taken over a 10-month period from December 2019 to September 2020.

Soils from these plots were used to inoculate Quercus rubra leaf litter in a lab microcosm experiment across different moisture treatments. Carbon mineralization was measured over 202 days by measuring CO2 production in each microcosm over 24 h at 17 time points (day 1, 6, 9, 13, 20, 27, 34, 43, 50, 64, 78, 92, 105, 120, 141, 168, 202) with the frequency of measurement decreasing over the course of the experiment. Cumulative C mineralization rates were calculated. To estimate CO2 evolved from Q. rubra litter, cumulative C mineralization from litter-soil microcosms were subtracted from soil-only controls for the corresponding microsite soil sample.

Usage notes

There are 4 associated CSVs in this dataset:

1. Micosite properties that describe the microsite by elevation, associated tree species, tree DBH, slope, and aspect.


2. microsite measurements that include site, plot, date sampled, sampling period name, soil temperature, litter temperature, soil gravimetric water content, soil pH, microbial biomass (SIR), soil %N, soil %C, soil C:N, bulk density (0-5cm), soil water holding capcity


3. microcosm experiment carbon mineralization time series that includes site, plot,,, replicate, day, date, lab treament, litter carbon mineralization, soil carbon mineralization


4. cumulative carbon mineralization from 202 day microcosm experiment that includes site, plot, treatment, replicate, litter cumulative carbon mineralization, and soil umulative carbon mineralization



There is one README file that describes the variables and units within each CSV.



National Science Foundation, Award: DEB-1926482

National Science Foundation, Award: DEB-1926413