Source: http://www.asmscience.org/content/book/10.1128/9781555817145.ch06
Timestamp: 2019-04-23 04:51:48+00:00

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Phylogenetic tree of Crenarchaeota based on 16S rRNA sequences (more than 800 bp, ≈800 sequences). Clades containing recognized candidate species and enrichment cultures are shown in black. Clades containing environmental clones potentially linking to ammonia oxidation are shown in gray. SAGMCG I, South African Gold Mine Crenarchaeotic Group I; HWCG, Hot Water Crenarchaeotic Group. Crenarchaeota Group I.1a is known as marine group I Crenarchaeota, and Group I.1b is known as soil Crenarchaeota.
Stoichiometry and kinetics of ammonia oxidation by N. maritimus. (A) Trace of oxygen uptake by aliquots of early-stationary phase cells (cell density, ~5.0 × 107 cells ml–1, 1 mM nitrite) obtained by microrespirometry. Ammonium added to resting cells was oxidized without significant lag time with a ratio of 1 mol of ammonium to 1.5 mol of O2. (B) Michaelis-Menten kinetics calculated from oxygen uptake rates (second part) in panel A.
Diagram of the N. maritimus circular chromosome. Rings, from outside to the center: 1, genes of forward strand (color by COG categories); 2, genes on reverse strand (color by COG categories); 3, RNA genes (tRNAs orange, rRNAs red, other RNAs black); 4, copper-containing protein genes (red); 5, genes involved in transcription and regulation (green); 6, genes annotated as transporters (blue); 7, putative ammonia-monooxygenase genes (silver); 8, G+C content; 9, GC skew.
Archaeal genome size and G+C content. Csym, C. symbiosum; Nmar, N. maritimus.
Synteny plot comparing N. maritimus and C. symbiosum genomes. The comparison was done in the protein level with the program Promer ( Kurtz et al., 2004 ). The DNA sequences were translated in all six reading frames and compared.
Amino acid utilization of the largest gene in N. maritimus and surface proteins. The data on surface proteins (n = 38) are adapted from Reva and Tümmler (2008) .
Relative contribution in COGs among representative Crenarchaea and AOB.
Organization of the amo gene clusters in archaeal and bacterial nitrifiers. Putative gene names and the N. maritimus gene locus numbers are shown within each ORF (gray arrows). The identification and size of proteins encoded in the N. maritimus locus are amoA (216 amino acids), hypothetical protein (120 amino acids), amoB (189 amino acids), and amoC (190 amino acids).
Proposed archaeal ammonia-oxidation pathway. NXOR, putative nitroxyl oxidoreductase; CuHAO, copper hydroxylamine oxidoreductase. The dashed line indicates the pathway having hydroxylamine as intermediate. Octagons containing Q and QH2 represent the oxidized and reduced quinone pool, respectively. Each complex is numbered: complex I, NADH:ubiquinone oxidoreductase; complex III, cytochrome c-ubiquinone oxidoreductase; complex IV, terminal oxidase; complex V, ATP synthase. Plastocyanin-like electron carriers are shown as hexagons containing pcy.
Alignment of copper-containing nitrite reductase/multicopper oxidase gene sequences (Nmar_1259 and 1667, annotated as nirK) with Global Ocean Sampling data sets and cultured microorganisms. Shading of amino acids: identical (white on black) and similar (black on gray) sequences.
Proposed autotrophic 3-hydroxypropionate/4-hydroxybutyrate pathway in N. maritimus. Enzymes catalyzing each reaction are numbered. Annotated genes are coded as a locus tag in parentheses.
Glycolysis and gluconeogenesis pathway of N. maritimus and the distribution of genes of enzymes involved in the process among some Archaea and Bacteria.
The first evidence of ectoine and hydroxyectoine biosynthesis in the Archaea. (A) Comparison of ectoine synthesis operon clusters with putative gene names. Microorganisms, except for Pseudomonas stutzeri, are of marine origin. Nmar_1346, ectA, l-2,4-diaminobutyric acid acetyltransferase; Nmar_1345, ectB, diaminobutyrate-2-oxoglutarate aminotransferase; Nmar_1344, ectC, ectoine synthase; Nmar_1343, thpD, ectoine hydroxylase; lysC, aspartate kinase. (B) Phylogenetic relationship of ectA gene. The evolutionary history was inferred using the neighbor-joining method. The evolutionary distances were computed using the JTT matrix-based method and are in the units of inferred amino acid substitutions per site. The scale bar shows 0.1 substitutions per site. The bootstrap values greater than 70% (1,000 replicates) are shown next to each node. There were a total of 130 positions in the final data set, and all positions containing gaps and missing data were eliminated from the data set.
Hierarchical clustering of N. maritimus and other archaeal genomes based on enzyme (A) and COG (B) clustering methods for the type of protein/functional families. The figures were prepared by using the genome-clustering tool in the integrated microbial genomes system ( Markowitz et al., 2006 , 2008 ). The placement in the tree reflects the distance between genomes, whereby the computed distance is based on the similarity of the functional characterization of genomes in terms of a specific protein/functional family. The enzyme-based clustering supports an affiliation of Nitrosopumilus and Cenarchaeum with the Crenarchaeota, whereas the COG-based clustering indicates that these two genera are of independent origin and possibly represent a novel kingdom (Thaumarchaeota).
Recruitment of GOS and HOT sequences to the N. maritimus genome. (A) All available data sets. (B) Pelagic data sets (sampling sites are deeper than 200 m). (C) Coastal data sets (sampling sites are shallower than 200 m). (D) Surface data sets (samples are collected shallower than 200 m). (E) Deep water data sets (samples are collected deeper than 200 m). (F) Pelagic and coastal data sets against N. europaea genome. Arrows indicate the position of 16S/23S rRNA genes.
Relative abundance of the number of reads in metagenomic libraries recruited to the N. maritimus genome. The number of reads in each metagenomic libraries is normalized by the obtained total number of reads (n = 5,773) in all libraries tested (reads are obtained from 58 libraries among 92 marine and freshwater libraries examined).
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