Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria

Axel Aigle, Cecile Gubry-Rangin, Cécile Thion, Katerina Estera-Molina, Heather Richmond, Jennifer Pett-Ridge, Mary K. Firestone, Graeme Nicol, James Prosser* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

20 Citations (Scopus)


Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.

Original languageEnglish
Pages (from-to)4032-4045
Number of pages14
JournalEnvironmental Microbiology
Issue number9
Early online date11 Aug 2020
Publication statusPublished - Sept 2020

Bibliographical note

Open Access via Wiley publishing agreement.
This work was financially supported by a Natural Environmental Research Council grant (NE/L006286/1). CGR and GWN were also supported, respectively, by a Royal Society University Research Fellowship (UF150571) and the AXA Research Fund. Research at LLNL was conducted under the auspices of DOE Contract DE‐AC52‐07NA27344, award SCW1632. We thank Dr Robin Walker for access to the pH plots at Craibstone, SRUC, Aberdeen.


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