Biodiversity and ecophysiology of ammonia-oxidizing bacteria
Aerobic ammonia-oxidizing bacteria (AOB) catalyze the first step of aerobic nitrification, the oxidation of ammonia (NH3) to nitrite (NO2-). They are highly important for the turnover of inorganic nitrogen in many ecosystems and for biological wastewater treatment.
Nitrifying bacteria detected by FISH in activated sludge (red: AOB, green: NOB).
| Comparative sequence analysis of 16S rRNA genes has been used to detect AOB in natural and engineered habitats and to study their phylogeny (e. g., Purkhold et al., 2000). Besides ribosomal RNA, the gene of the alpha subunit of ammonia monooxygenase (amoA) is suitable as phylogenetic and also as functional marker for the specific detection and identification of AOB in the environment (Holmes et al., 1995; Purkhold et al., 2000). Laborious screening of amoA gene libraries for sequences related to AOB is unnecessary as this gene is restricted to these organisms. Therefore, PCR-mediated amplification of amoA genes followed by cloning and sequence analyses is an effective approach to assess the biodiversity of AOB in nature. Our comprehensive collections of 16S rRNA and amoA gene sequences are continually updated and provide the basis for phylogeny and for designing and evaluating AOB-specific PCR primers and oligonucleotide probes (Mobarry et al., 1996; Koops et al., 2003).
|
Biodiversity surveys based on comparative sequence analyses are affected by biases of DNA extraction, PCR, and cloning. For example, Juretschko et al. (1998) used fluorescence in situ hybridization (FISH) with rRNA-targeted probes and found Nitrosococcus mobilis to be the dominant AOB in a wastewater treatment plant while all amoA sequences retrieved from the same plant were affiliated to Nitrosomonas europaea. We apply FISH as powerful tool to detect AOB (e.g., Wagner et al., 1995), to study their spatial localization in environmental samples (Figure), and to determine their population structure (by combining FISH with semi-automated quantification via  confocal microscopy and digital image analysis). However, in a number of habitats like soil or sediments strong background autofluorescence and low cellular ribosome content hamper the use of FISH to detect AOB and other bacteria.
Many limitations of FISH are overcome by rRNA-targeted oligonucleotide microarrays. We are developing a novel, AOB-specific oligonucleotide microarray (the AOB-PhyloChip). The high degree of parallelization offered by microarrays will enable us to screen environmental samples for all known AOB in a single assay. In a second step, the AOB-PhyloChip will be extended to a Nitrifier-PhyloChip that covers also nitrite-oxidizing bacteria and anaerobic ammonium oxidizers.
We are also interested in the ecophysiology and in situ activity of AOB. In contrast to certain other bacteria, the cellular ribosome content of AOB does not correlate with metabolic activity. Thus rRNA-targeted FISH is inappropriate to distinguish active from inactive AOB in situ (Morgenroth et al., 2000). We are testing whether probes that target intergenic spacer regions (ISR) on the rRNA operon can identify active AOB. ISR-targeted probes have already been used to detect active anaerobic ammonium oxidizing bacteria (Schmid et al., 2001).
Please follow these links for a general introduction on nitrifying bacteria or for more information about our work on nitrite-oxidizing bacteria.
Investigated by: Holger Daims, Kilian Stoecker, Frank Maixner, Roland Hatzenpichler, Gertrude Wegl, Anneliese Müller
Selected literature:
- Holmes, A. J., Costello, A., Lidstrom, M. E. and Murrell, J. C. (1995). Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol. Lett. 132.
- Juretschko, S., Timmermann, G., Schmid, M., Schleifer, K.-H., Pommering-Röser, A., Koops, H.-P. and Wagner, M. (1998). Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl. Environ. Microbiol. 64: 3042-3051.
- Koops, H. P., Purkhold, U., Pommerening-Röser, A., Timmermann, G. and Wagner, M. (2003). The lithoautotrophic ammonia oxidizers. In: The Prokaryotes: An evolving electronic resource for the microbiological community. M. Dworkin et al. (Ed.), Springer Verlag, New York.
- Mobarry, B. K., Wagner, M., Urbain, V., Rittmann, B. E. and Stahl, D. A. (1996). Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 62: 2156-2162.
- Morgenroth, E., Obermayer, A., Arnold, E., Brühl, A., Wagner, M. and Wilderer, P. A. (2000). Effect of long-term idle periods on the performance of sequencing batch reactors. Wat. Sci. Tech. 41: 105-113.
- Purkhold, U., Pommering-Röser, A., Juretschko, S., Schmid, M. C., Koops, H.-P. and Wagner, M. (2000). Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 66: 5368-5382.
- Schmid, M., Schmitz-Esser, S., Jetten, M. and Wagner, M. (2001). 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ. Microbiol. 3: 450-459.
- Wagner, M., Rath, G., Amann, R., Koops, H.-P. and Schleifer, K.-H. (1995). In situ identification of ammonia-oxidizing bacteria. System. Appl. Microbiol. 18: 251-264.
|
