Microbial flexibility

As an essential building block of amino acids, proteins and DNA, nitrogen is key to life on Earth. Nitrogen is also the main constituent of our atmosphere, but the main form it takes, N₂, is unusable by almost all living organisms but a few select microbes. Instead, most living creatures, from bacteria to primates, rely on nitrogen that has been bound in oxides, as ammonia or in organic compounds. Many microbes actually make a living by cycling nitrogen from one fixed state to another: they gain energy using various nitrogen species as electron donors and receptors.

Credit: © PHOTOALTO / ALAMY

One part of the nitrogen cycle is nitrification, in which bacteria and archaea oxidize ammonia, and nitrite-oxidizing bacteria convert nitrite to nitrate. One of the most widespread genera of these nitrite-oxidizing bacteria is Nitrospira, with species occurring in oxic oceans, soils, hot springs and even wastewater treatment plants. However, Nitrospira appears to alternatively be able to perform anaerobic respiration, with H₂ as an electron donor and nitrite as an electron acceptor. Culture experiments and genetic sequencing now suggest that Nitrospira moscoviensis can also use H₂ as an energy source for aerobic respiration when nitrite is not available (Science 345, 1052–1054; 2014).

Holger Daims and colleagues observed cultures of N. moscoviensis growing with no nitrite available, as long as H₂ and O₂ were present. The uptake of CO₂ by these microbes occurred even when H₂ concentrations were low, but no net growth occurred. This indicates that only a fraction of the cells in the culture were highly metabolically active under these conditions.

Genome sequencing of N. moscoviensis identified a series of genes associated with the hydrogen oxidizing enzyme hydrogenase, known as the hup locus. The best explanation for the appearance of these genes in N. moscoviensis is lateral gene transfer from a different phylum of bacteria. Intriguingly, the hup locus only appears in one of the phylogenetic lineages of Nitrospira (lineage II), suggesting that either only this lineage acquired the gene through lateral gene transfer or that the gene was later lost by lineage I.

The ability of N. moscoviensis to remain metabolically active without the continued presence of nitrite provides a strong ecological advantage, and probably explains why Nitrospira can be found in some low oxygen environments with available H₂, such as rice paddies, deep hydrothermal fields and hot springs.