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Abstract Soil microbial communities play critical roles in various ecosystem processes, but studies at a large spatial and temporal scale have been challenging due to the difficulty in finding the relevant samples in available data sets as well as the lack of standardization in sample collection and processing. The National Ecological Observatory Network (NEON) has been collecting soil microbial community data multiple times per year for 47 terrestrial sites in 20 eco‐climatic domains, producing one of the most extensive standardized sampling efforts for soil microbial biodiversity to date. Here, we introduce the neonMicrobe R package—a suite of downloading, preprocessing, data set assembly, and sensitivity analysis tools for NEON’s newly published 16S and ITS amplicon sequencing data products which characterize soil bacterial and fungal communities, respectively. neonMicrobe is designed to make these data more accessible to ecologists without assuming prior experience with bioinformatic pipelines. We describe quality control steps used to remove quality‐flagged samples, report on sensitivity analyses used to determine appropriate quality filtering parameters for the DADA2 workflow, and demonstrate the immediate usability of the output data by conducting standard analyses of soil microbial diversity. The sequence abundance tables produced byneonMicrobecan be linked to NEON’s other data products (e.g., soil physical and chemical properties, plant community composition) and soil subsamples archived in the NEON Biorepository. We provide recommendations for incorporatingneonMicrobeinto reproducible scientific workflows, discuss technical considerations for large‐scale amplicon sequence analysis, and outline future directions for NEON‐enabled microbial ecology. In particular, we believe that NEON marker gene sequence data will allow researchers to answer outstanding questions about the spatial and temporal dynamics of soil microbial communities while explicitly accounting for scale dependence. We expect that the data produced by NEON and theneonMicrobeR package will act as a valuable ecological baseline to inform and contextualize future experimental and modeling endeavors.
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NEON distributed initial soil characterization dataset (DP1.10047.001) modified for statistical analysis of organic carbon and extractable metals in Hall and Thompson (2021)
We compiled National Ecological Observatory Network (NEON) datasets related to the initial distributed soil sampling effort and subsetted them (removed samples with missing values for certain variables, and several samples with extreme values) for use in statistical analyses to describe relationships between soil organic carbon (SOC) and metals measured in several soil chemical extractions. The NEON provisional data products we used were DP1.10047.001 and DP1.10008.001, which were subsequently combined by NEON as a single data product DP1.10047.001, “Soil physical and chemical properties, distributed initial characterization”. These datasets were used for the analyses reported in a manuscript by Hall and Thompson (2021) in the Soil Science Society of America Journal.
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- Award ID(s):
- 1802745
- PAR ID:
- 10387430
- Publisher / Repository:
- Environmental Data Initiative
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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