Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria

Abstract

We have conducted a preliminary phylogenetic survey of ammonia-oxidizing ␤-proteobacteria, using 16S rRNA gene libraries prepared by selective PCR and DNA from acid and neutral soils and polluted and nonpolluted marine sediments. Enrichment cultures were established from samples and analyzed by PCR. Analysis of 111 partial sequences of c. 300 bases revealed that the environmental sequences formed seven clusters, four of which are novel, within the phylogenetic radiation defined by cultured autotrophic ammonia oxidizers. Longer sequences from 13 cluster representatives support their phylogenetic positions relative to cultured taxa. These data suggest that known taxa may not be representative of the ammonia-oxidizing ␤-proteobacteria in our samples. Our data provide further evidence that molecular and culture-based enrichment methods can select for different community members. Most enrichments contained novel Nitrosomonaslike sequences whereas novel Nitrosospira-like sequences were more common from gene libraries of soils and marine sediments. This is the first evidence for the occurrence of Nitrosospira-like strains in marine samples. Clear differences between the sequences of soil and marine sediment libraries were detected. Comparison of 16S rRNA sequences from polluted and nonpolluted sediments provided no strong evidence that the community composition was determined by the degree of pollution. Soil clone sequences fell into four clusters, each containing sequences from acid and neutral soils in varying proportions. Our data suggest that some related strains may be present in both samples, but further work is needed to resolve whether there is selection due to pH for particular sequence types.

Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land‐use types

“…In contrast, our sequences grouped into two of seven proposed AOB clusters (i.e. clusters three and six from Stephen et al 1996), and each land-use type harboured AOB from both of these clusters. The difference between the two studies may be due to the low-intensity management of the pastures in our study.…”

“…The other cluster was most related to Nitrosospira multiformis and contained 333 sequences and 37 OTUs (OTUs 20-56). These clusters correspond to clusters six and three of Stephen et al (1996), respectively. The most abundant OTU (OTU #20) contained 94 individual sequences and was most closely affiliated with the genus Nitrosospira.…”

“…Most past research has been based on laboratory isolates, which are known to represent a small proportion of environmental microorganisms (Ward et al 1990;Smith et al 2001). A few recent studies have utilized culture-independent molecular techniques to study AOB distributions, and these studies suggest that AOB can vary among different environments and can be sensitive to human management (Stephen et al 1996;Bruns et al 1999;McCaig et al 1999;Phillips et al 2000;Webster et al 2002). However, very few of these studies have made statistical, quantitative comparisons of AOB diversity or composition across different environmental systems, and none have examined whether AOB vary with changes in plant species or plant species diversity while other variables remain constant.…”

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

“…Autotrophic nitrification occurs in acid soils, despite the inability of cultivated bacterial ammonia oxidizers to grow in liquid batch culture at pH values below 7. Previous studies provided evidence for selection of different ammonia oxidizer phylotypes in soils maintained in the pH range 4.5-7.5 since 1961 (Stephen et al, 1996;Kowalchuk et al, 1998). This study aimed to determine whether similar selection occurred for ammonia oxidizing archaea in these soils and whether bacterial ammonia oxidizer selection persisted since the previous study performed 10 years earlier.…”

Loss of diversity of ammonia‐oxidizing bacteria correlates with increasing salinity in an estuary system

“…Previous studies of AOB diversity in freshwater and marine systems suggest some overlap of AOB species distribution, but these systems appear to be dominated by distinctly different communities (Hiorns et al ., 1995;Stephen et al ., 1996;Hastings et al ., 1998;Speksnijder et al ., 1998;Phillips et al ., 1999). Ammonia-oxidizing bacteria species distribution in estuaries, however, may be more complex, primarily because of seasonally and spatially varying mixtures of fresh and marine waters.…”