Multi-factorial drivers of ammonia oxidizer communities: Evidence from a national soil survey

Huaiying Yao*, Colin D. Campbell, Stephen J. Chapman, Thomas E. Freitag, Graeme W. Nicol, Brajesh K. Singh

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

114 Citations (Scopus)


The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different ammonia oxidizers, we used samples (n=713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40-45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13-16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main ammonia oxidizers in acidic soils. However, for AOB, soil pH and substrate (ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning.

Original languageEnglish
Pages (from-to)2545-2556
Number of pages12
JournalEnvironmental Microbiology
Issue number9
Early online date2 May 2013
Publication statusPublished - Sept 2013

Bibliographical note

This work was financially supported by the Royal Society of Edinburgh, and the National Science Foundation of China (No. 31071869, 31272256, 41090283). C.D.C., S.J.C. and T.E.F. are funded by the Scottish Government, Rural and Environment Research and Analysis Directorate. is supported by Grain and Cotton Research Development Corporation and Australian Research Council (DP130104841). Lucinda Robinson, Nadine Thomas and Duncan White are gratefully acknowledged for their technical assistance and advice. We thank Jane Hall at CEH Bangor for access to the nitrogen (NHx and NOx) deposition data.


Dive into the research topics of 'Multi-factorial drivers of ammonia oxidizer communities: Evidence from a national soil survey'. Together they form a unique fingerprint.

Cite this