Nitrososphaera viennensis is a soil microorganism belonging to the domain Archaea. It plays a specialized role in its environment by deriving energy from converting ammonia into nitrite, a process with major ecological implications. This function provides a window into the complex biogeochemical cycles that sustain life.
Archaea and Their Role in Earth’s Nitrogen Cycle
The tree of life has three main domains: Bacteria, Eukarya, and Archaea. Archaea were once thought to be “extremophiles” living only in harsh conditions, but they are now known to be widespread in nearly every environment. Although single-celled like bacteria, many of their core proteins are more similar to those found in eukaryotes.
This diverse domain is deeply involved in Earth’s nutrient cycles. The nitrogen cycle is the process where nitrogen, a component of proteins and DNA, is converted between various chemical forms. One step in this cycle is nitrification, which begins with the oxidation of ammonia. For many years, specific bacteria were thought to be solely responsible for this process.
The discovery that certain archaea also perform this function reshaped scientific understanding. These ammonia-oxidizing archaea (AOA) are now recognized as major contributors to nitrification, especially in environments with low ammonia concentrations like the open ocean and many soils. By converting ammonia (NH3) into nitrite (NO2-), AOA make nitrogen more accessible for other organisms and play a role in ecosystem health.
Discovering Nitrososphaera viennensis in the Soil
Nitrososphaera viennensis was first isolated from a soil sample taken from the gardens of the University of Vienna. This was noteworthy as few non-extremophilic archaea had been successfully cultivated in a lab at the time. Its distinction required the creation of a new genus (Nitrososphaera), family, order, and class.
The strain EN76T became the first AOA isolated in a pure culture from soil. Its habitat is soil, where AOA like N. viennensis can account for up to 1% of the total microbes. It occupies the niche of a chemolithoautotroph, deriving energy from inorganic chemical reactions and using inorganic carbon to build its cellular components.
The cells are irregularly shaped cocci, measuring 0.6 to 0.9 micrometers in diameter. Electron microscopy reveals an S-layer, a crystalline protein shell, with a p3 symmetry previously seen only in some hyperthermophilic archaea. This unique cellular structure, combined with its distinct genetic makeup, underscores its evolutionary separation from other known ammonia oxidizers.
The Unique Metabolism of Nitrososphaera viennensis
As an obligate aerobe, Nitrososphaera viennensis requires oxygen to live and fuels itself by oxidizing ammonia to nitrite. The energy released powers all its life functions. The organism is also capable of using urea, a common nitrogen-containing compound in soil, as an alternative energy source.
This metabolic process relies on the enzyme complex ammonia monooxygenase (AMO). The archaeal AMO is related to the bacterial version but has distinct properties. The N. viennensis AMO enzyme relies on copper as a cofactor, and its genome contains genes for multiple subunits of this enzyme. Its function is to oxidize ammonia to hydroxylamine, though the subsequent steps to produce nitrite are still being detailed.
Its metabolic activity also produces nitrous oxide (N2O), a potent greenhouse gas, as a byproduct. The organism’s growth is inhibited by high concentrations of ammonia, its own fuel, and it does not grow in concentrations at or above 20 mM. This highlights its adaptation to low-ammonia environments.
Genomic Insights into an Ammonia Oxidizer
The genome of Nitrososphaera viennensis is 2.52 million base pairs (Mb) and contains 3,123 predicted protein-coding genes. This is larger than the genomes of its more streamlined marine relatives, suggesting the soil environment requires a more versatile genetic toolkit.
Comparative genomics reveals a core set of 860 genes shared among all known AOA. These genes are responsible for fundamental metabolic pathways, including the AMO enzyme subunits and pathways for fixing carbon dioxide. Proteomic studies show that under laboratory conditions, N. viennensis expresses nearly 50% of its predicted genes.
The genome also contains specific adaptations for soil life. These include genes for:
- Cell surface modifications
- Cell adhesion
- Biofilm formation
- Detoxifying certain aromatic compounds
These features reflect its adaptation to a complex and variable terrestrial habitat.
Studying Nitrososphaera viennensis: Challenges and Importance
Studying Nitrososphaera viennensis in the lab presents several challenges. The organism has an optimal growth temperature of around 42°C and prefers a neutral pH of 7.5. Its slow growth rate is a defining characteristic. Compared to bacteria that can divide in minutes, N. viennensis grows much more slowly, which makes experiments time-consuming and results in low yields of biomass.
Early cultivation efforts found that adding small amounts of organic acids like pyruvate enhanced its growth. It was later determined these compounds scavenge damaging reactive oxygen species, allowing the organism to grow in a purely autotrophic manner.
As a representative of a major group of soil archaea, it provides insights into the biology of this domain. Research on this microbe enhances our understanding of soil fertility, the nitrogen cycle, and the production of greenhouse gases. Its unique physiology and genetics help scientists piece together the roles of archaea in shaping the environment.