Joshua P. Schimel | Search USGS

USGS2020

An open source database for the synthesis of soil radiocarbon data: ISRaD version 1.0

Radiocarbon is a critical constraint on our estimates of the timescales of soil carbon cycling that can aid in identifying mechanisms of carbon stabilization and destabilization and improve the forecast of soil carbon response to management or environmental change. Despite the wealth of soil radiocarbon data that have been reported over the past 75 years, the ability to apply these data to global-scale questions is limited by our capacity to synthesize and compare measurements generated using a variety of methods. Here, we present the International Soil Radiocarbon Database (ISRaD; http://soilradiocarbon.org , last access: 16 December 2019), an open-source archive of soil data that include reported measurements from bulk soils, distinct soil carbon pools isolated in the laboratory by a variety of soil fractionation methods, samples of soil gas or water collected interstitially from within an intact soil profile, CO 2 gas isolated from laboratory soil incubations, and fluxes collected in situ from a soil profile. The core of ISRaD is a relational database structured around individual datasets (entries) and organized hierarchically to report soil radiocarbon data, measured at different physical and temporal scales as well as other soil or environmental properties that may also be measured and may assist with interpretation and context. Anyone may contribute their own data to the database by entering it into the ISRaD template and subjecting it to quality assurance protocols. ISRaD can be accessed through (1) a web-based interface, (2) an R package (ISRaD), or (3) direct access to code and data through the GitHub repository, which hosts both code and data. The design of ISRaD allows for participants to become directly involved in the management, design, and application of ISRaD data. The synthesized dataset is available in two forms: the original data as reported by the authors of the datasets and an enhanced dataset that includes ancillary geospatial data calculated within the ISRaD framework. ISRaD also provides data management tools in the ISRaD-R package that provide a starting point for data analysis; as an open-source project, the broader soil community is invited and encouraged to add data, tools, and ideas for improvement. As a whole, ISRaD provides resources to aid our evaluation of soil dynamics across a range of spatial and temporal scales. The ISRaD v1.0 dataset is archived and freely available at https://doi.org/10.5281/zenodo.2613911 (Lawrence et al., 2019).

Earth System Science Data↗

USGS2015

Linking microbial community structure and microbial processes: An empirical and conceptual overview

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

FEMS Microbiology Ecology↗