Abstract
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.
Highlights
Niche specialization and differentiation are wellestablished concepts in ecology and play roles in establishment of plant and animal communities and species coexistence (Harper et al, 1961; Schoener, 1974)
They coexist in most terrestrial ecosystems studied and perform the same ecosystem function, oxidation of soil ammonia, which has significant impacts on soil biogeochemistry, nitrate pollution, fertilizer loss, nitrous oxide production and control of soil nitrification rate (Hink et al, 2018; Prosser and Nicol, 2012). Laboratory cultures of both groups grow chemolithoautotrophically, fixing carbon dioxide and gaining energy through oxidation of ammonia to nitrite. Both groups possess related genes encoding ammonia monooxygenase (AMO), which catalyses the conversion of ammonia to hydroxylamine, and amoA, encoding subunit A, is the standard marker gene for ammonia oxidisers
Physiological characteristics including substrate affinity for ammonia (Kits et al, 2017) and maximum specific growth rate ranges (Prosser and Nicol, 2012) of newly enriched or isolated cultures of AOB activity (AOA) and Ammonia oxidizing bacteria (AOB) from soil are similar. Despite their similarities, AOA and AOB belong to different domains, the Archaea and the Bacteria, and major differences in fundamental aspects of their cell biology and physiology have been seen as potential reasons for niche specialization
Summary
Niche specialization and differentiation are wellestablished concepts in ecology and play roles in establishment of plant and animal communities and species coexistence (Harper et al, 1961; Schoener, 1974). Archaeal and bacterial ammonia oxidisers (AOA and AOB) have been extensively studied utilizing a range of approaches and are a useful model for investigation of niche specialization in microbial communities (GubryRangin et al, 2011; Prosser and Nicol, 2012) They coexist in most terrestrial ecosystems studied and perform the same ecosystem function, oxidation of soil ammonia, which has significant impacts on soil biogeochemistry, nitrate pollution, fertilizer loss, nitrous oxide production and control of soil nitrification rate (Hink et al, 2018; Prosser and Nicol, 2012). They differ in pathways for CO2 fixation (Könneke et al, 2014), cell wall structure (Albers and Meyer, 2011) and pathways for oxidation of ammonia (Kozlowski et al, 2016)
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