Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology

Abstract

The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important in the global cycling of nitrogen. These organisms are unique in their ability to use the conversion of ammonia to nitrite as their sole energy source. Because of the importance of this functional group of bacteria, understanding of their ecology and physiology has become a subject of intense research over recent years. The monophyletic nature of these bacteria in terrestrial environments has facilitated molecular biological approaches in studying their ecology, and progress in this field has been rapid. The ammonia-oxidizing bacteria of the beta-subclass Proteobacteria have become somewhat of a model system within molecular microbial ecology, and this chapter reviews recent progress in our knowledge of their distribution, diversity, and ecology.

The Biogeography of Ammonia-Oxidizing Bacterial Communities in Soil

“…2), with all of these Nitrosomonas-like sequences clustering within the N. communis lineage defined by Purkhold et al [5]. These results are consistent with other studies that have shown the dominance of Nitrosospira AOB in terrestrial environments [4,10,18,39,40]. If we examine the proportional occurrence or abundance of Nitrosomonas-like AOB versus Nitrosospira-like AOB in each clone library, we find that nitrosomonads were particularly abundant in the desert soils (MD2, MD3, MD5) where they represented >75% of the sequences in these clone libraries (Fig.…”

“…The abundance of nitrosomonads in desert soils may also be related to soil salinity (which was not measured but which is often higher in desert than in non-desert soils), given that nitrosomads are often halophilic [41]. Although it has been hypothesized that nitrosomonads are likely to become relatively more abundant in soils with high N availability [10,42], our results do not support this hypothesis; we found no significant correlations between the proportional representation of nitrosomonads in the libraries and any of the measured soil and site parameters listed in Table 2 (ρ<0.2, P>0.4 in all cases), including those estimates of soil N availability (extractable NH 4 + concentrations, total dissolved inorganic N concentrations, and net N mineralization rates). However, it is important to note that nearly all of our sites are nonagricultural and have not received high fertilizer inputs so the N availability levels in our soils may be far lower than in soils analyzed in previous studies.…”

“…Likewise, results from previous studies [14][15][16]20] have contributed to the hypothesis that representatives of Nitrosospira cluster 3 are likely to be relatively more abundant in soils with higher levels of N availability. If we examine the proportional abundances of Nitrosospira cluster 3, we see no correlations with our measured indices of N availability (N mineralization rates and extractable NH 4 + or the sum of NH 4 + plus NO 3 − concentrations, P>0.4 in all cases). Either we did not quantify a specific N pool or flux these organisms are sensitive to, or it is not valid to assume that N availability drives the relative abundance of Nitrosospira cluster 3 in soil AOB communities across such a broad range of different ecosystem types.…”

“…Although there are a number of published exceptions, Nitrosospira cluster 2 is often considered to dominate in acidic soils [4,18,37]. However, while Nitrosopira cluster 2 was relatively abundant in three forest soil libraries (BF1, BZ2, BZ3) with reasonably low pHs (4.05-5.36), there was no overall correlation between the relative abundances of cluster 2 in the libraries and soil pH (ρ=0.15, P=0.3) suggesting that cluster 2 AOB do not necessarily have higher relative abundances in acidic soils.…”

“…This limitation is less problematic when examining the distribution of individual bacterial taxa, which can be studied at reasonably fine levels of phylogenetic resolution. The ammonia-oxidizing bacteria, represented by the Nitrosomonas and Nitrosospira genera within the betasubclass of the Proteobacteria [4], are particularly well suited for examining the distribution of soil microbes in space as the phylogenetic relationships within the ammoniaoxidizing bacteria (AOB) are reasonably well described [5]. In addition, unlike many other bacterial taxa found in soil, the group is represented by a relatively large number of cultured isolates.…”