Using network analysis to explore co-occurrence patterns in soil microbial communities
Top Cited Papers
- 8 September 2011
- journal article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 6 (2), 343-351
- https://doi.org/10.1038/ismej.2011.119
Abstract
Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160 000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly.Keywords
This publication has 51 references indexed in Scilit:
- The under-recognized dominance of Verrucomicrobia in soil bacterial communitiesSoil Biology and Biochemistry, 2011
- Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communitiesThe ISME Journal, 2010
- Examining the global distribution of dominant archaeal populations in soilThe ISME Journal, 2010
- QIIME allows analysis of high-throughput community sequencing dataNature Methods, 2010
- A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analysesThe ISME Journal, 2009
- Pyrosequencing enumerates and contrasts soil microbial diversityThe ISME Journal, 2007
- Global patterns in bacterial diversityProceedings of the National Academy of Sciences of the United States of America, 2007
- Microbial diversity in the deep sea and the underexplored “rare biosphere”Proceedings of the National Academy of Sciences of the United States of America, 2006
- Modularity and community structure in networksProceedings of the National Academy of Sciences of the United States of America, 2006
- Functional cartography of complex metabolic networksNature, 2005