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Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps

  • Soil Microbiology
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Abstract

We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.

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Acknowledgments

MD thanks Dr. Martin Steen Mortensen for assistance with the robot soil extraction and Luma George Odish for laboratorial assistance in the preparation of the Illumina library. Dr. Samuel Jacquiod helped with advice and assistance for the statistical calculations. We also thank Stefan Kellerer and Klaus Kellner, the wardens of the Tröglhütte of the DAV (Deutscher Alpenverein), for making our stay at the field site pleasant. We wish to express general gratitude to researchers for sharing their data and programming codes as well as engaging in online discussion forums (particularly Stack Overflow), which has benefited the analysis in this study.

Funding

Funding for this study was provided in the frame of a Ph.D. position for MD within the Research Training Group RESPONSE (RTG 2010), supported by the Deutsche Forschungsgemeinschaft (DFG).

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Authors and Affiliations

  1. Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, 17487, Greifswald, Mecklenburg-Vorpommern, Germany

    Mathilde Borg Dahl & Martin Schnittler

  2. Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Asker Daniel Brejnrod, Jakob Russel & Søren Johannes Sørensen

Authors
  1. Mathilde Borg Dahl
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  2. Asker Daniel Brejnrod
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  3. Jakob Russel
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  4. Søren Johannes Sørensen
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  5. Martin Schnittler
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Corresponding author

Correspondence to Mathilde Borg Dahl.

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The authors declare that they have no conflict of interest.

Electronic Supplementary Material

ESM 1

List of primers used to amplify the three target communities. (XLSX 9 kb)

ESM 2

DNA reads of mock samples. (XLSX 32 kb)

ESM 3

Sample quality: Illumina quality statistics, OTU accumulation curves, and overview of significant relations between the numbers of DNA reads and the numbers of OTUs. (PDF 2149 kb)

ESM 4

OTU tables. (XLSX 2472 kb)

ESM 5

Maximum-likelihood phylogenetic tree of the most abundant myxomycete OTUs. (PDF 1432 kb)

ESM 6

Analysis script. (PDF 98 kb)

ESM 7

Result script. (PDF 115 kb)

ESM 8

Functional classification. (XLSX 14 kb)

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Borg Dahl, M., Brejnrod, A.D., Russel, J. et al. Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps. Microb Ecol 78, 764–780 (2019). https://doi.org/10.1007/s00248-019-01347-1

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  • DOI: https://doi.org/10.1007/s00248-019-01347-1

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