Sedlacek, Christopher J

Nitrobacterstrain NHB1 is a nitrite-oxidising bacterium previously co-enriched with the neutrophilic ammonia-oxidising bacteriumNitrosospiraAHB1, a consortium that nitrifies in acidic conditions in co-culture. Here we characterise the growth of the isolateNitrobacterstrain NHB1 as a function of pH and nitrite (NO2-) concentration, and its influence on the activity of acidophilic soil ammonia-oxidising archaea (AOA). NHB1 is acidotolerant and grows optimally at pH 6.0 (range 5.0 - 7.5) at initial NO2-concentrations of 500 μM. However, the optimum decreases to pH 5.0 at lower initial NO2-concentrations typically found in soil, with detectable growth down to pH 3.5. NHB1 has a comparatively high affinity for NO2-with an apparent-half-saturation constant (54 μM) one order of magnitude lower than its closest relative, the neutrophilic strainNitrobacter hamburgensisX14. In co-culture, NHB1 enhances the growth of acidophilic AOA. Specifically,Nitrosotalea devaniterraeNd1 andNitrosotalea sinensisNd2 are sensitive to NO2--derived compounds and only oxidise ~200-300 μM ammonia (NH3) in batch cultures. However, in co-culture with NHB1, pH ranges were lowered by ~0.5 pH units and both strains could oxidise up to 3 mM NH3, only limited by buffering capacity. NHB1 possesses a cyanase facilitating reciprocal cross-feeding via generating cyanate-derived NH3and utilising AOA-derived NO2-. Removal of NO2-is likely crucial for the growth of nitrifiers in acidic soils and this study highlights the importance of considering substrate and metabolic product concentrations when characterising physiology. Genome analysis reveals NHB1 is distinct from validated species and the name "Nitrobacter laanbroekii" is proposed.

AbstractAmmonia-oxidizing archaea (AOA) within the phylumThaumarchaeaare the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from theNitrosocaldusclade, group 1.1b and group 1.1aThaumarchaeain terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50 °C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a novelThaumarchaeonfrom the deep-branchingNitrosocaldaceaefamily of which we have obtained a high (∼85 %) enrichment from biofilm of an Icelandic hot spring (73 °C). This AOA, which we provisionally refer to as “CandidatusNitrosocaldus islandicus”, is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 °C and 70 °C.Ca.N. islandicus encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks anirKgene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent asCa.N. islandicus is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed thatCa.N. islandicus has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase(iorAB)as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizingThaumarchaea.Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.