Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor

Abstract

Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor. The pure culture of N. mobilis Ms1 was cultivated in liquid mineral medium with 30 mg-N L-1 (2.14 mM) of ammonium at room temperature under dark conditions. The optimum growth of N. mobilis Ms1 occurred at 27°C and pH 8, with a maximum growth rate of 0.05–0.07 h-1, which corresponded to a generation time of 10–14 h. The half saturation constant for ammonium uptake rate and the maximum ammonium uptake rate of N. mobilis Ms1 were 30.70 ± 0.51 μM NH4+ and 0.01 ± 0.002 pmol NH4+ cells-1 h-1, respectively. N. mobilis Ms1 had higher ammonia oxidation activity than N. europaea in this study. The oxygen uptake activity kinetics of N. mobilis Ms1 were Km(O2) = 21.74 ± 4.01 μM O2 and V max(O2) = 0.06 ± 0.02 pmol O2 cells-1 h-1. Ms1 grew well at ammonium and NaCl concentrations of up to 100 and 500 mM, respectively. The nitrite tolerance of N. mobilis Ms1 was extremely high (up to 300 mM) compared to AOB previously isolated from activated sludge and wastewater treatment plants. The average nucleotide identity between the genomes of N. mobilis Ms1 and other Nitrosomonas species indicated that N. mobilis Ms1 was distantly related to other Nitrosomonas species. The organization of the genes encoding protein inventory involved in ammonia oxidation and nitrifier denitrification processes were different from other Nitrosomonas species. The current study provides a needed physiological and genomic characterization of N. mobilis-like bacteria and a better understanding of their ecophysiological properties, enabling comparison of these bacteria with other AOB in wastewater treatment systems and natural ecosystems.

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

“…The metabolic function of this type of hydrogenase in complete nitrifiers remains to be determined and might include (i) H 2 oxidation as alternative or additional electron source for energy conservation and/or CO 2 fixation, (ii) H 2 evolution for maintaining the redox balance during anaerobic degradation of simple organic matter (as suggested by Kits et al 2017), and (iii) H 2 S production for sulfur assimilation. Moreover, the identification of group 3b hydrogenases in canonical ammonia and nitrite oxidizer genomes, like the marine NOB Nitrococcus mobilis (Füssel et al 2017), Nitrospina marina (Lücker et al 2013), and several AOB including Nitrosococcus halophilus Nc4 (GenBank accession number ADE14678.1) and Nitrosomonas mobilis (Thandar et al 2016) emphasizes the need to characterize the physiological function(s) of this enzyme in nitrifying bacteria. N. moscoviensis is the only Nitrospira species known to have recruited a different type of hydrogenase.…”

Transcriptome Analysis of the Ammonia-Oxidizing Bacterium <i>Nitrosomonas mobilis</i> Ms1 Reveals Division of Labor between Aggregates and Free-living Cells

“…The quality of the reads was improved using CLC genomics workbench (CLC Bio) by trimming the rest of the adapter, low quality reads (limit 0.05), short reads (>15 bp), and one base from the 5′ and 3′ ends. Reads were also mapped under the conditions of Mismatch cost 2, Insertion cost 3, Deletion cost 3, Length fraction 0.5, and Similarity fraction 0.8 to the N. mobilis Ms1 genome sequence (Accession numbers FMWO01000001-FMWO01000112) (Thandar et al, 2016). Based on read count data, a hierarchical clustering analysis was performed using the Bioconductor package TCC.…”

“…Strains and culture conditions N. mobilis Ms1 isolated from nitrifying granules was cultured in a batch mode with mineral medium containing 2.1 mM NH 4 Cl as previously reported (Fujitani et al, 2015;Thandar et al, 2016). Inorganic medium included NaCl (0.116 g L -1 ), MgSO 4 ·7H 2 O (0.4 g L -1 ), CaCl 2 ·2H 2 O (0.073 g L -1 ), KCl (0.038 g L -1 ), KH 2 PO 4 (0.034 g L -1 ), FeCl 2 (0.002 g L -1 ), EDTA (0.0043 g L -1 ), MnCl 2 ·4H 2 O (0.1 mg L -1 ), CoCl 2 ·6H 2 O (0.024 mg L -1 ), NiCl 2 ·6H 2 O (0.024 mg L -1 ), CuCl 2 ·2H 2 O (0.017 mg L -1 ), ZnCl 2 (0.068 mg L -1 ), Na 2 WO 4 ·2H 2 O (0.033 mg L -1 ), Na 2 MoO 4 (0.024 mg L -1 ), and H 3 BO 3 (0.062 mg L -1 ).…”

“…N. mobilis Ms1 was isolated from nitrifying granules in the form of aggregates and formed aggregates even in pure cultures (Fujitani et al, 2015). One of the distinct physiological properties of N. mobilis Ms1 is tolerance to high concentrations of ammonia and nitrite (Thandar et al, 2016). Genomic information was also obtained (Thandar et al, 2016).…”

“…One of the distinct physiological properties of N. mobilis Ms1 is tolerance to high concentrations of ammonia and nitrite (Thandar et al, 2016). Genomic information was also obtained (Thandar et al, 2016).…”