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. 2017 Jul 25:4:170092.
doi: 10.1038/sdata.2017.92. eCollection 2017.

A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting

Roland C Wilhelm  1 , Erick Cardenas  1 , Hilary Leung  1 , Kendra Maas  1 , Martin Hartmann  2 , Aria Hahn  1 , Steven Hallam  1 , William W Mohn  1
Affiliations

A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting

Roland C Wilhelm et al. Sci Data. .

Abstract

The scarcity of long-term data on soil microbial communities in the decades following timber harvesting limits current understanding of the ecological problems associated with maintaining the productivity of managed forests. The high complexity of soil communities and the heterogeneity of forest and soil necessitates a comprehensive approach to understand the role of microbial processes in managed forest ecosystems. Here, we describe a curated collection of well replicated, multi-faceted data from eighteen reforested sites in six different North American ecozones within the Long-term Soil Productivity (LTSP) Study, without detailed analysis of results or discussion. The experiments were designed to contrast microbial community composition and function among forest soils from harvested treatment plots with varying intensities of organic matter removal. The collection includes 724 bacterial (16S) and 658 fungal (ITS2) amplicon libraries, 133 shotgun metagenomic libraries as well as stable isotope probing amplicon libraries capturing the effects of harvesting on hemicellulolytic and cellulolytic populations. This collection serves as a foundation for the LTSP Study and other studies of the ecology of forest soil and forest disturbance.

Keywords: Forest ecology; Metagenomics; Molecular ecology; Soil microbiology.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Locations of soil sampling and descriptions of data collection conducted for this study.
The locations and names of eighteen North American sampling sites are shown grouped into six ecozones. The term ‘ecozone’ is used to refer to the distinct local assemblages of organisms and climatic factors between groupings of sites. An overview of the design for soil sampling along with data collection are superimposed on the map. OM removal treatments are shaded according to the intensity of OM removal.
Figure 2
Figure 2. Plot conditions immediately following harvesting (year zero) in the PPCA ecozone.
These photographs capture the initial variation in the amount of organic matter (OM) removal at plots which were sampled 11–17 years for this study. Plots like these were replicated at three sites within every ecozone [photo credit: Dr Matt Busse; mbusse@fs.fed.us
Figure 3
Figure 3. The successful enrichment and recovery of 13C-enriched DNA in SIP experiments.
The assimilation of 13C by functional guilds during stable isotope probing experiments was evident in (a) the total 13C-enrichment of soil DNA extract and (b) recovery of DNA from the densest CsCl gradient fractions (F1-F7). These differences were evident in comparing soils amended with either 12C- (unlabelled) or 13C-cellulose. These trends were apparent in both cellulose and hemicellulose SIP experiments. Boxplots depict the average (centre line) and spread (from 25th to 75th percentile) of data, while the whiskers extend to the extrema. A total of twelve samples were averaged for each factor.
See this image and copyright information in PMC

References

Data Citations

    1. 2015. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/search?query=PRJEB8599
    1. 2016. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/search?query=PRJEB12501
    1. 2015. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/search?query=PRJEB8420
    1. 2015. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/search?query=PRJEB9181
    1. 2015. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/search?query=PRJEB9182

References

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