A marine coculture of archaeal ammonia and bacterial nitrite oxidizers enriched from the North Sea

Archaeal ammonia oxidizers (AOA) are considered main contributors to marine nitrogen cycling but cultured representatives are few and their cultivation is time and labor-intensive. In this study, AOA from the North Sea were cultured together with their nitrite-oxidizing bacterial (NOB) partners in a reactor system under low ammonia, nitrite and oxygen concentrations to mimic natural conditions. Increasing the influent substrate concentration in a stepwise manner, while carefully managing substrate and product levels in the reactor, resulted in a final ammonia oxidation rate of 350 µmoles·L-1·day-1. Measurements of ammonia, nitrite and nitrate demonstrated that both ammonia oxidation and nitrite oxidation occurred in the reactor and ammonia was almost completely converted to nitrate. Metagenomic sequencing revealed the presence of an AOA (Candidatus Nitrosarchaeum marinum), most closely related to Candidatus Nitrosarchaeum limnium, and a, likely new species of, Nitrospina NOB. Results from quantitative PCR targeting archaeal 16S rRNA genes showed a steady increase in AOA cell numbers following the increase in ammonia oxidation activity up to 2.4·108 archaeal cells·ml-1. This is the first report of a successful enrichment of a representative of the genus Nitrosarchaeum using a high salinity medium and the establishment of a stable AOA-NOB co-culture. The reactor cultivation methodology adopted in this study provides a relatively easy and time efficient way of cultivating AOA which may serve as means to generate sufficient AOA biomass for physiological and co-culture experiments.