The idea that oxidation of ammonia to nitrate is in fact a biological process was first given by Louis Pasteur in 1862. Later in 1875, Alexander Müller, while conducting a quality assessment of water from wells in Berlin, noted that ammonium was stable in sterilized solutions but nitrified in natural waters. A. Müller put forward, that nitrification is thus performed by microorganisms. In 1877, Jean-Jacques Schloesing and Achille Müntz, two French agricultural chemists working in Paris, proved that nitrification is indeed microbially mediated process by the experiments with liquid sewage and artificial soil matrix (sterilized sand with powdered chalk). Their findings were confirmed soon (in 1878) by Robert Warington who was investigating nitrification ability of garden soil at the Rothamsted experimental station in Harpenden in England. R. Warington made also the first observation that nitrification is a two-step process in 1879 which was confirmed by John Munro in 1886. Although at that time, it was believed that two-step nitrification is separated into distinct life phases or character traits of a single microorganism.
The first pure nitrifier (ammonia-oxidizing) was most probably isolated in 1890 by Percy Frankland and Grace Frankland, two English scientists from Scotland. Before that, Warington, Sergei Winogradsky and the Franklands were only able to enrich cultures of nitrifiers. Frankland and Frankland succeeded with a system of serial dilutions with very low inoculum and long cultivation times counting in years. Sergei Winogradsky claimed pure culture isolation in the same year (1890), but his culture was still co-culture of ammonia- and nitrite-oxidizing bacteria. S. Winogradsky succeeded just one year later in 1891.
In fact, during the serial dilutions ammonia-oxidizers and nitrite-oxidizers were unknowingly separated resulting in pure culture with ammonia-oxidation ability only. Thus Frankland and Frankland observed that these pure cultures lose ability to perform both steps. Loss of nitrite oxidation ability was observed already by R. Warington. Cultivation of pure nitrite oxidizer happened later during 20th century, however it is not possible to be certain which cultures were without contaminants as all theoretically pure strains share same trait (nitrite consumption, nitrate production).