Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm

Andrea K. Bartram, Xingpeng Jiang, Michael D. J. Lynch, Andre P. Masella, Graeme W. Nicol, Jonathan Dushoff, Josh D. Neufeld*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

115 Citations (Scopus)


Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects of pH on individual bacterial taxa within bacterial communities, both abundant and rare. We collected composite soil samples over 2 years from an experimentally maintained pH gradient ranging from 4.5 to 7.5 from the Craibstone Experimental Farm (Craibstone, Scotland). Extracted nucleic acids were characterized by bacterial and group-specific denaturing gradient gel electrophoresis and next-generation sequencing of bacterial 16S rRNA genes. Both methods demonstrated comparable and reproducible shifts within higher taxonomic bacterial groups (e.g. Acidobacteria, Alphaproteobacteria, Verrucomicrobia, and Gammaproteobacteria) across the pH gradient. In addition, we used non-negative matrix factorization (NMF) for the first time on 16S rRNA gene data to identify positively interacting (i.e. co-occurring) operational taxonomic unit (OTU) clusters (i.e. ‘components’), with abundances that correlated strongly with pH, and sample year to a lesser extent. All OTUs identified by NMF were visualized within principle coordinate analyses of UNIFRAC distances and subjected to taxonomic network analysis (SSUnique), which plotted OTU abundance and similarity against established taxonomies. Most pH-dependent OTUs identified here would not have been identified by previous methodologies for microbial community profiling and were unrelated to known lineages.

Original languageEnglish
Pages (from-to)403-415
Number of pages13
JournalFEMS Microbiology Ecology
Issue number2
Early online date25 Oct 2013
Publication statusPublished - Feb 2014

Bibliographical note

The authors gratefully acknowledge SRUC (Aberdeen) for
access to the Craibstone pH plots. A.K.B. was supported
by an Ontario Graduate Scholarship from the Government
of Ontario. This research was supported by a Discovery
Grant from the Natural Sciences and Engineering
Research Council of Canada (NSERC).


  • 16S rRNA genes
  • Agriculture
  • Microbial diversity
  • PH
  • Rare biosphere
  • Soil bacteria


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