Components of the nitrogen metabolism of <i>Ca</i>. N. evergladensis

<p>: 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.</p

Comparison of protein coding sequences (CDS) of <i>Ca</i>. Nitrososphaera evergladensis with CDS of other ammonia-oxidizing archaea.

<p>(A) CDS of <i>Ca</i>. Nitrososphaera evergladensis were compared to CDS of <i>Ca</i>. N. gargensis. (B) CDS of the group I.1a (<i>N. maritimus</i>, <i>Ca</i>. N. sediminis, <i>C. symbiosum</i>, <i>Ca</i>. N. limnia, <i>Ca</i>. N. koreensis) were compared to CDS of the group I.1b (<i>Ca</i>. N. evergladensis and <i>Ca</i>. N. gargensis). Overlapping regions represent CDS with amino acid sequence identity 35% and higher.</p

Organization of (A) urease and urea transporter genes; (B) ammonia monooxygenase gene order of <i>Ca</i>. N. evergladensis; (C) flagella and chemotaxis genes in the present genome.

<p>Organization of (A) urease and urea transporter genes; (B) ammonia monooxygenase gene order of <i>Ca</i>. N. evergladensis; (C) flagella and chemotaxis genes in the present genome.</p

Genome synteny alignments of <i>Ca</i>. N. evergladensis, (A) <i>Ca</i>. N. gargensis and (B) <i>N. maritimus</i>.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101648#pone.0101648-Kurtz1" target="_blank">[114]</a>. 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.</p

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.

<p>* components of TS found by TIGRfam database.</p

A phylogenetic tree of ammonia-oxidizing archaea 16S rRNA gene sequences (about 1.4 kb).

<p>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).</p

Genome Sequence of <i>Candidatus</i> Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea

<div><p>The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon <i>Candidatus</i> Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The <i>de novo</i> assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. <i>Ca</i>. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative <i>Ca</i>. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.</p></div