Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures

• Published in: Applied and Environmental Microbiology 2003-10, Vol.69 (10), p.6152-6164
• Main Authors: Avrahami, S, Conrad, R
• Format: Article
• Language: English
• Subjects: acid soils; alkaline soils; Ammonia; Ammonia - metabolism; ammonia monooxygenase; Ammonia oxidizers; amoA gene; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - metabolism; biological activity in soil; Biological and medical sciences; Cloning, Molecular; community structure; denaturing gradient gel electrophoresis; Ecosystem; Electrophoresis - methods; Fertilizers; Fundamental and applied biological sciences. Psychology; grassland soils; Hydrogen-Ion Concentration; Long term; Microbial Ecology; Microbiology; Molecular Sequence Data; nitrification; Nitrosomonadaceae; Nitrosospira; Nitrospira; nucleotide sequences; Oxidation; Oxidation-Reduction; Oxidoreductases - genetics; oxygenases; Phylogeny; Poaceae; Polymerase Chain Reaction; Sequence Analysis, DNA; soil bacteria; soil biology; soil ecology; Soil Microbiology; soil temperature; Soils; structural genes; Temperature
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.69.10.6152-6164.2003

The effect of temperature on the community structure of ammonia-oxidizing bacteria was investigated in three different meadow soils. Two of the soils (OMS and GMS) were acidic (pH 5.0 to 5.8) and from sites in Germany with low annual mean temperature (about 10°C), while KMS soil was slightly alkaline (pH 7.9) and from a site in Israel with a high annual mean temperature (about 22°C). The soils were fertilized and incubated for up to 20 weeks in a moist state and as a buffered (pH 7) slurry amended with urea at different incubation temperatures (4 to 37°C). OMS soil was also incubated with less fertilizer than the other soils. The community structure of ammonia oxidizers was analyzed before and after incubation by denaturing gradient gel electrophoresis (DGGE) of the amoA gene, which codes for the subunit of ammonia monooxygenase. All amoA gene sequences found belonged to the genus Nitrosospira. The analysis showed community change due to temperature both in moist soil and in the soil slurry. Two patterns of community change were observed. One pattern was a change between the different Nitrosospira clusters, which was observed in moist soil and slurry incubations of GMS and OMS. Nitrosospira AmoA cluster 1 was mainly detected below 30°C, while Nitrosospira cluster 4 was predominant at 25°C. Nitrosospira clusters 3a, 3b, and 9 dominated at 30°C. The second pattern, observed in KMS, showed a community shift predominantly within a single Nitrosospira cluster. The sequences of the individual DGGE bands that exhibited different trends with temperature belonged almost exclusively to Nitrosospira cluster 3a. We conclude that ammonia oxidizer populations are influenced by temperature. In addition, we confirmed previous observations that N fertilizer also influences the community structure of ammonia oxidizers. Thus, Nitrosospira cluster 1 was absent in OMS soil treated with less fertilizer, while Nitrosospira cluster 9 was only found in the sample given less fertilizer.