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From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?

  • Dorsaf Kerfahi
  • Binu M. Tripathi
  • Ke Dong
  • Mincheol Kim
  • Hyoki Kim
  • J. W. Ferry Slik
  • Rusea Go
  • Jonathan M. Adams
Soil Microbiology

Abstract

Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon “classical” views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.

Keywords

Arctic Functional genes Shotgun metagenomics Microbial diversity Tropics 

Notes

Funding Information

This work was partly supported by a grant from the Polar Academic Program (PAP) funded by Korea Polar Research Institute (KOPRI) under the number 0409-20140091. This work was also partly supported by a grant from the National Research Foundation (NRF) funded by the Korean government, Ministry of Education, Science and Technology (MEST) under the number NRF-0409-20150076.

Supplementary material

248_2018_1215_MOESM1_ESM.docx (1.9 mb)
ESM 1 (DOCX 1906 kb)
248_2018_1215_MOESM2_ESM.docx (22 kb)
ESM 2 (DOCX 21 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Dorsaf Kerfahi
    • 1
  • Binu M. Tripathi
    • 2
  • Ke Dong
    • 1
  • Mincheol Kim
    • 2
  • Hyoki Kim
    • 3
  • J. W. Ferry Slik
    • 4
  • Rusea Go
    • 5
  • Jonathan M. Adams
    • 6
  1. 1.Department of Biological SciencesSeoul National UniversitySeoulRepublic of Korea
  2. 2.Korea Polar Research InstituteIncheonRepublic of Korea
  3. 3.Celemics Inc.SeoulRepublic of Korea
  4. 4.Faculty of ScienceUniversiti Brunei DarussalamGadongBrunei Darussalam
  5. 5.Department of Biology, Faculty of SciencesUniversiti Putra MalaysiaSerdangMalaysia
  6. 6.Division of Agrifood and Environment, School of Water, Energy and EnvironmentCranfield UniversityBedfordshireUK

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