Biodiversity and ecophysiology of nitrite-oxidizing bacteria

Nitrite-oxidizing bacteria (NOB) catalyze the second step of aerobic nitrification, the oxidation of nitrite (NO₂^-) to nitrate (NO₃^-). According to textbook knowledge, Nitrobacter species are the main NOB in most natural habitats and in biological wastewater treatment. These Nitrobacter species are relatively easy to cultivate and can be isolated from many environmental samples. Only recently, cultivation-independent methods revealed that novel, yet uncultured NOB are far more important than Nitrobacter in wastewater treatment plants (Burrell et al., 1998; Juretschko et al., 1998; Schramm et al., 1998). These bacteria belong to the genus Nitrospira, which is part of the bacterial phylum Nitrospirae (Ehrich et al., 1995), and are not related to Nitrobacter.

Uncultured Nitrospira-like bacteria have meanwhile been found in many habitats, including freshwater and marine environments, soil, and the rhizosphere (e. g., Bartosch et al., 2002). The large diversity and high abundance of Nitrospira-like bacteria in natural habitats and in wastewater treatment plants indicate that these NOB are very competitive and adaptable and play key roles for nitrogen cycling in many ecosystems.

The ecophysiology of uncultured Nitrospira-like bacteria is studied in order to understand their natural functions, to optimize the performance of wastewater treatment plants, and to better control the nitrite-oxidizing activity in agricultural soils where NOB are partly responsible for significant nitrogen losses. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is used to detect Nitrospira-like bacteria in complex environmental samples (Fig. 1). The set of Nitrospira-specific probes is continually extended to cover novel lineages within the genus Nitrospira (Daims et al., 2001a). Quantitative FISH with these and additional probes, which detect Nitrobacter, other NOB, or ammonia oxidizers, provides detailed insight into the population structure of nitrifying communities (Daims et al., 2001b). Different environmental samples are screened by 16S rRNA sequence analyses for Nitrospira-like bacteria to obtain a more detailed picture of their phylogeny and natural distribution.

The physiology of uncultured Nitrospira-like bacteria is investigated by combined FISH and microautoradiography (FISH-MAR). This approach has already revealed that Nitrospira-like bacteria living in activated sludge are autotrophs (fix CO₂), which use also pyruvate under aerobic conditions. These findings indicate that Nitrospira-like bacteria can use inorganic as well as some organic carbon sources, and may benefit from the increased availability of organic carbon in wastewater or other habitats (Daims et al., 2001a). A novel extension of FISH allows measuring absolute cell concentrations of tightly clustered bacteria like Nitrospira in complex sludge or biofilm samples by

confocal laser scanning microscopy and digital image analysis (Daims et al., 2001c). Per-cell nutrient conversion rates can be estimated based on these cell densities and bulk measurements of substrate turnover.

Our in situ functional analyses of Nitrospira-like bacteria are complemented by

environmental genomics. Data obtained by cloning and sequencing large genome fragments of uncultured Nitrospira-like bacteria provide new insight into the biology of these elusive organisms.

Please follow these links for a

general introduction on nitrifying bacteria or for more information about our work on

ammonia-oxidizing bacteria.

Investigated by:

Holger Daims,

Kilian Stoecker,

Frank Maixner,

Karin Hace,

Sebastian Lücker,

Roland Hatzenpichler,

Gertrude Wegl

Selected literature:

Bartosch, S., Harttwig, C., Spieck, E. and Bock, E. (2002). Immunological detection of Nitrospira-like bacteria in various soils. Microb. Ecol. 43: 26-33.
Burrell, P. C., Keller, J. and Blackall, L. L. (1998). Microbiology of a nitrite-oxidizing bioreactor. Appl. Environ. Microbiol. 64: 1878-1883.
Daims, H., Nielsen, J. L., Nielsen, P. H., Schleifer, K. H. and Wagner, M. (2001a). In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl. Environ. Microbiol. 67: 5273-5284.
Daims, H., Purkhold, U., Bjerrum, L., Arnold, E., Wilderer, P. A. and Wagner, M. (2001b). Nitrification in sequencing biofilm batch reactors: lessons from molecular approaches. Wat. Sci. Tech. 43: 9-18.
Daims, H., Ramsing, N. B., Schleifer, K.-H. and Wagner, M. (2001c). Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl. Environ. Microbiol. 67: 5810-5818.
Ehrich, S., Behrens, D., Lebedeva, E., Ludwig, W. and Bock, E. (1995). A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch. Microbiol. 164: 16-23.
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.
Schramm, A., de Beer, D., Wagner, M. and Amann, R. (1998). Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl. Environ. Microbiol. 64: 3480-3485.

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