Figure 1.
Correlation of ammonia oxidation with the growth of Ca. Nitrososphaera evergladensis enrichment culture incubated for 21 days.
(A) Concentrations of ammonia and nitrite were determined spectrophotometrically. (B) Archaeal amoA gene copies were measured by quantitative PCR.
Figure 2.
A phylogenetic tree of ammonia-oxidizing archaea 16S rRNA gene sequences (about 1.4 kb).
23 16S rRNA sequences of AOA were randomly selected from the National Center for Biotechnology Information databases. Conservative sites (1.08 kb) were selected using Gblocks. The branching patterns in the maximum-likelihood tree are denoted by their respective bootstrap values (1000 iterations).
Figure 3.
Comparison of protein coding sequences (CDS) of Ca. Nitrososphaera evergladensis with CDS of other ammonia-oxidizing archaea.
(A) CDS of Ca. Nitrososphaera evergladensis were compared to CDS of Ca. N. gargensis. (B) CDS of the group I.1a (N. maritimus, Ca. N. sediminis, C. symbiosum, Ca. N. limnia, Ca. N. koreensis) were compared to CDS of the group I.1b (Ca. N. evergladensis and Ca. N. gargensis). Overlapping regions represent CDS with amino acid sequence identity 35% and higher.
Figure 4.
Genome synteny alignments of Ca. N. evergladensis, (A) Ca. N. gargensis and (B) N. maritimus.
Axes X and Y represent topology of coding sequences in the comparing genomes. Entire genomes were compared by MUMmer 3.0 package using Promer tool [114]. Each dot represents a match of at least six amino acids from compared genomes. Forward matching amino acid sequences are plotted as red lines/dots while reverse are plotted as blue lines/dots. A line of dots with slope = 1 represents an undisturbed segment of conservation between the two sequences, while a line of slope = −1 represents an inverted segment of conservation between the two sequences.
Figure 5.
Organization of (A) urease and urea transporter genes; (B) ammonia monooxygenase gene order of Ca. N. evergladensis; (C) flagella and chemotaxis genes in the present genome.
Figure 6.
Components of the nitrogen metabolism of Ca. N. evergladensis
: ammonia oxidation (4, 5), ammonia assimilation (8, 9, 10), nitrite reduction (6), nitrous oxide production (7). Reactions are mediated by the following transporters and enzymes: urea transporters, urease (1, 2), ammonia transporters (3), archaeal ammonia monooxygenase (AMO) (4), candidate enzyme: multicopper oxidase (5), nitrite reductase (NirK) (6), nitric oxide reductase (NorD, NorQ), catalytic subunit (NorB) is missing (7), glutamate dehydrogenase (8), glutamine synthetase (9), glutamate synthase (10). NO may upregulate activity of AMO. * - experimental evidences are needed.
Table 1.
Two component systems (TS) identified in the genomes of AOA representatives from the group I.1a, I.1b and AOB using Conserved Domain Search and TIGRfam database.
Figure 7.
Distribution of Clusters of Orthologous Groups (COGs) in the AOA genomes from soil group I.1b and I.1a.
COGs represented with higher copy number in the group I.1b than in the group I.1a were selected by Ttest (Pvalue<0.05). Error bars display standard deviation.