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

• Published in: Environmental microbiology 2020-09, Vol.22 (9), p.4032-4045
• Main Authors: Aigle, A., Gubry‐Rangin, C., Thion, C., Estera‐Molina, K. Y., Richmond, H., Pett‐Ridge, J., Firestone, M. K., Nicol, G. W., Prosser, J. I.
• Format: Article
• Language: English
• Subjects: Abundance; Ammonia; Ammonia - metabolism; AmoA gene; Archaea; Archaea - genetics; Archaea - isolation & purification; Archaea - metabolism; Bacteria; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; BASIC BIOLOGICAL SCIENCES; Biodiversity and Ecology; Environmental changes; ENVIRONMENTAL SCIENCES; GEOSCIENCES; Hydrogen-Ion Concentration; Hypotheses; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Life Sciences; Microbial activity; Microbiology and Parasitology; Microbiota; Microcosms; Microorganisms; Niche overlap; Niches; Nitrification; Oxidation; Oxidation-Reduction; Perturbations; pH effects; Soil; Soil - chemistry; Soil characteristics; Soil investigations; Soil Microbiology; Soil temperature; Soil testing; Soils; Specialization; Stable isotopes; Temperature; Temperature effects; Transcription
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.15192

Summary 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.