Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils

Abstract

Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in microcosms containing natural and managed grasslands and amended with artificial sheep urine, a major factor determining local ammonia concentrations in these environments. Nitrification kinetics were assessed by analysis of changes in urea, ammonia, nitrite and nitrate concentrations and ammonia oxidizer communities were characterized by analysis of 16S rRNA genes amplified from extracted DNA using ammonia oxidizer-specific primers. In natural soils, ammonia oxidizer community structure determined the delay preceding nitrification, which depended on the relative abundance of two Nitrosospira clusters, termed 3a and 3b. In batch cultures, pure culture and enrichment culture representatives of Nitrosospira 3a were sensitive to high ammonia concentration, while Nitrosospira cluster 3b representatives and Nitrosomonas europaea were tolerant. Delays in nitrification occurred in natural soils dominated by Nitrosospira cluster 3a and resulted from the time required for growth of low concentrations of Nitrosospira cluster 3b. In microcosms dominated by Nitrosospira cluster 3b and Nitrosomonas, no substantial delays were observed. In managed soils, no delays in nitrification were detected, regardless of initial ammonia oxidizer community structure, most probably resulting from higher ammonia oxidizer cell concentrations. The data therefore demonstrate a direct link between bacterial community structure, physiological diversity and ecosystem function.

Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure

“…This is consistent with results of Patra et al (2006) who observed that grazing-induced changes in ammonia availability explained changes in nitrifier activity and community structure at these study sites under field conditions. Furthermore, the preliminary shift in community structure observed before any change in activity is consistent with results reported by Webster et al (2005), who observed that, in natural, ungrazed soils, a change in AOB community structure was often required before enhancement of nitrification following sheep urine application. The authors suggested that, when AOB communities were dominated by strains sensitive to high ammonia concentration, a shift toward ammonia-tolerant AOB populations was needed to allow nitrification increase.…”

“…(1) to compare the speed and extent of changes in the activity, abundance and community structure of nitrifiers for two years after switches in grassland management to or from grazing, testing the hypothesis that disturbance of a previously undisturbed system would lead to a faster response than cessation of disturbance of a previously disturbed system; (2) to assess the ability of changes in the community structure and abundance of nitrifiers to explain observed changes in nitrification under these two scenarios, in particular whether changes in nitrification levels first required changes in nitrifier community structure as suggested by Webster et al (2005) and (3) to evaluate the relative importance of past and current grazing regimes on the activity, abundance and community structure of nitrifiers two years after a change in grazing regime.…”

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms

“…Analysis of AOB sequences demonstrated that Nitrosospira cluster 3 phylotypes were the most responsive in the highest amendment. Organisms within this lineage are commonly found in agricultural soils (Stephen et al, 1996), with some populations being tolerant to relatively high ammonia concentrations (Webster et al, 2005). Interestingly, in the 16S rRNA gene DGGE profiles, an additional faint band (highlighted band 1) increased in relative intensity in the highest amendment, which belonged to an organism placed within the Nitrosomonas oligotropha lineage with high sequence similarity (98%) to Nitrosomonas ureae.…”

The Biogeography of Ammonia-Oxidizing Bacterial Communities in Soil

“…In addition, the AOB, along with the ammonia-oxidizing archaea [6,7], perform a rate-limiting step of nitrification and play a key role in the regulation of soil nitrogen dynamics. For this reason, the study of AOB biogeography may have direct relevance to studies of soil biogeochemistry given that distinct AOB groups are likely to have different physiological and ecological attributes [8].…”