1. A B C
Supplementary Figure S1 Fluorescence microscopy of cultures enriched with TAO100. Cultures were stained with DAPI (a), FITC-labeled DNA probe for eubacterial 16S rRNA (b), and Cy3-labeled DNA probe for TAO100 16S rRNA (c). Images are from the same field of view. Scale bar, 10 mm.

2. Nitrosococcus watsonii C-113 AF153343
Nitrosococcus oceani ATCC19707 NC007484
Nitrosococcus halophilus Nc4 AF287298
TAO100
Thiocapsa roseatype DSM235T AJ002798
Thiolamprovum pedioforme DSM3802 Y12297
Chromatium okenii DSM169 AJ223234
Rhabdochromatium marinum X84316
Halochromatium salexigens 6310T X98597
Thiorhodovibrio winogradskyistrain SSP1 AJ006214
Nitrococcus mobilis ATCC25380 L35510
Arhodomonas aquaeolei ATCC49307 M26631
Halorhodospira halophila M26630
Thioalcalovibrio denitrificans AF126545
Thiorhodospira sibirica AT12 AJ006530
Ectothiorhodospira mobilis DSM237 X93481
Ectothiorhodospira shaposhnikovi M59151
Thiobacillus halophilus U58020
Halothiobacillus hydrothermalis M90662
Halothiobacillus neapolitanus DSM581 AF173169
Halothiobacillus kellyi AF170419
Acidithiobacillus thiooxidans strain ATCC19377 AJ459803
Thermithiobacillus tepidarius DSM3134 AJ459801
100 93 92 77 86 99 60 65 54 53 56
0.02
Chromatiaceae
Ectothiorhodospiraceae
Halothiobacillaceae
Acidothiobacillales a
Gammaproteobacteria PmoA
Gammaproteobacteria AmoA
Alphaproteobacteria PmoA
Betaproteobacteria AmoA
Methylomonas methanica MC09 AEF98753
Methylosarcina lacus WP
Methylomarinovum caldicuralii BAF62078
TAO100
Nitrosococcus halophilus WP
Nitorsococcus watsonii C-113 AAF03938
Nitrosococcus oceani ATCC19707 AAB57809
Methylocystis sp. SC2 CCJ05654
Methylosinus trichosporium OB3b AAA87220
Methylocapsa acidiphila CAJ01617
Nitrosomonas eutropha C91　ABI60300
Nitrosomonas europaea ATCC19718 CAD84855
Nitrosospira multiformis ATCC25196 ABB76052　
Nitrosospira briensis C-128 AAB38709
Nitrosopumilus maritimus SCM1 ABY89139
100 99 94 80 59 71 93 60
0.2 b
Supplementary Figure S2 Phylogenetic relationships of TAO100 and related strains. (a) Phylogenetic relationships of TAO100, three g-AOB isolates, and relatives from three families in order Chromatiales and class Gammaproteobacteria, as inferred from 16S rRNA gene sequences (ca.1500 bp). (b) Phylogenetic relationships among amino acid sequences (165 residues) of ammonia monooxygenase subunit A (AmoA) and methane monooxygenase subunit A (PmoA). Trees were constructed using the neighbor-joining algorithm with Kimura two-parameter correction. Marked nodes are supported by bootstrap values greater than 45% by neighbor-joining. Scale bar, 0.02 nucleotide (a) and 0.2 amino acid (b) change per position.

3. a
TAO100 b
TAO100
Nitrosococcus
halophilus Nc4
oceani ATCC19707
watsonii C133
Nitrosospira
mutiformis
ATCC25196
Nitrosomonas
eutropha C91
europaea
ATCC19718
Genome size (bp)
2,018,314
4,145,260
3,522,111
3,373,286
3,234,309
2.781,824
2,812,094
GC basesa
42.1
51.6
50.3
50.1
53.9
48.5
50.7
ORFs
1,839
3,769
3,138
2,924
2,864
2,555
2,574
rRNA genes 5S 2 1
16S
23S
tRNA 44 46 45 43 41
Plasmid 3
aGC base % of chromosome was shown.
Supplementary Figure S3 Genome features of TAO100. (a) Circulars representation of the TAO100 chromosome and plasmid pTAO101. The distribution of CDSs is depicted by colored boxes according to the functional category of the KEGG modules and the direction of transcription (the outer circle is the plus strand; the inner circle is the minus strand. Light gray, KEGG Orthology (KO) not assigned in pathway; light purple, cellular processes; dark blue, environmental information processing; gray, no KO assigned; yellow-green, genetic information processing; tan, human diseases; black, hypothetical; light pink, metabolism; light orange, organismal systems; light blue, cellular processes, environmental information processing). The third and fourth circles indicate the distribution of rRNA and tRNA in the genome, respectively. (b) Table depicting the genome features of TAO100 and genome-sequenced AOB. Data were obtained from NCBI genome data base (

4. N. oceani
N. watsonii
N. halophilus
TAO100
Supplementary Figure S4 Venn diagram depicting the distribution of common and unique open reading frames (ORFs) among TAO100, N. halophilus, N. oceani and N. watsonii. Only complete protein-coding ORFs, including hypothetical unknowns, are included. The IS element, phage ORFs, and pseudogenes are excluded.

5. TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
TAO100
N.halophilus
N. oceani
N.watosoni
Supplementary Figure S5 Comparative genome analysis of TAO100. Alignment of the core genomes of TAO100 and three halophilic g-AOB belonging to the genus Nitrosococcus. Rows and columns represent genomes and orthologous groups, respectively. A black line indicates adjacent groups. A green line indicates non-adjacent neighbors (i.e., insertions are present), and a red line represents inversion. A total of 2,241 orthologous genes common to half of four strains were identified using MBGD.