Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons

PLoS One. 2016 Nov 18;11(11):e0165987. doi: 10.1371/journal.pone.0165987. eCollection 2016.


Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. In particular, we still have limited knowledge of how diverse functional groups of fungi interact with each other in facilitative and competitive ways in soil. Based on the high-throughput sequencing data of fungi in a cool-temperate forest in northern Japan, we analyzed how taxonomically and functionally diverse fungi showed correlated fine-scale distributions in soil. By uncovering pairs of fungi that frequently co-occurred in the same soil samples, networks depicting fine-scale co-occurrences of fungi were inferred at the O (organic matter) and A (surface soil) horizons. The results then led to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi could form compartmentalized (modular) networks of facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.

MeSH terms

  • Biodiversity
  • Computational Biology / methods
  • DNA Barcoding, Taxonomic
  • DNA, Ribosomal Spacer
  • Ecosystem
  • Fungi* / classification
  • Fungi* / genetics
  • Japan
  • Metagenome
  • Metagenomics / methods
  • Soil Microbiology*


  • DNA, Ribosomal Spacer

Grant support

This work was financially supported by Japan Society for the Promotion of Science JSPS KAKENHI Grant (No. 26711026) [] to HT; the Supporting Program for Interaction-based Initiative Team Studies (SPIRITS) by Kyoto University [ service/topic/spirits/lists/h27list_e/] to HT; [] of "PRESTO by JST (No. 11118); and the Funding Program for Next Generation World-Leading Researchers of Cabinet Office, the Government of Japan (GS014) to HT []. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.