Supporting Information

Table_SM1. Bacterial strains used for the construction of the community genome array

Groups / Species# / Strains/genes / G+C Content / Source
g-proteobacteria / Shewanella algae / BrY / 52-55 / Z.J & T.J’s collection
g-proteobacteria / Shewanella pealeana / ANG-SQ1 / 45 / Z.J & T.J’s collection
g-proteobacteria / Shewanella algae / OK-1 / 52-55 / Z.J & T.J’s collection
g-proteobacteria / Shewanella amazonensis / SB2B / 52 / Z.J & T.J’s collection
g-proteobacteria / Shewanella woodyi / MS32 / 39 / Z.J & T.J’s collection
g-proteobacteria / Shewanella oneidensis / MR-1 / 45 / Z.J & T.J’s collection
g-proteobacteria / S. oneidensis / MR-4 / 45 / Z.J & T.J’s collection
b-proteobacteria / Azoarcus tolulyticus / Td-1 / 69.3 / Z.J & T.J’s collection
b-proteobacteria / A. tolulyticus / Td-2 / 67.8 / Z.J & T.J’s collection
b-proteobacteria / A. tolulyticus / Td-3 / 68.5 / Z.J & T.J’s collection
b-proteobacteria / A. tolulyticus / Td-15 / 68.0* / Z.J & T.J’s collection
b-proteobacteria / A. tolulyticus / Td-17 / 66.9 / Z.J & T.J’s collection
b-proteobacteria / A. tolulyticus / Td-19 / 67.3 / Z.J & T.J’s collection
b-proteobacteria / A. tolulyticus / Td-21 / 68.6 / Z.J & T.J’s collection
b-proteobacteria / Azoarcus sp. / BL-11 / 67.4 / Z.J & T.J’s collection
b-proteobacteria / A. indigens / VB22T / 68.0* / Z.J & T.J’s collection
g-proteobacteria / Shewanella sp. / A8-3 / 49* / Marine isolate
g-proteobacteria / Pseudomonas stutzeri / B2-2 / 63.0* / Marine isolate
g-proteobacteria / Halomonas variabilis / B9-12 / 65.2* / Marine isolate
a-proteobacteria / a-proteobacterium / C1-4 / -- / Marine isolate
g-proteobacteria / P. stutzeri / C5-1 / 63.0* / Marine isolate
g-proteobacteria / Marinobacter sp. / C10-5 / 55.7 / Marine isolate
g-proteobacteria / Marinobacter sp. / D3-15 / 55.7 / Marine isolate
Gram positive / Staphylococcus saprophyticus / D3-16 / 37* / Marine isolate
g-proteobacteria / Marinobacter sp. / D5-10 / 55.7 / Marine isolate
g-proteobacteria / P. stutzeri / D7-6 / 63.0* / Marine isolate
g-proteobacteria / P. stutzeri / D8-12 / 63.0* / Marine isolate
g-proteobacteria / Marinobacter sp. / E1-7 / 55.7 / Marine isolate
g-proteobacteria / P. stutzeri / E4-2 / 63.0* / Marine isolate
Gram positive bacteria / Bacillus methanolicus / F6-2 / 43* / Marine isolate
Gram positive bactria / B. methanolicus / F7-3 / 43* / Marine isolate
g-proteobacteria / P. stutzeri / F9-1 / 63.0* / Marine isolate
g-proteobacteria / P. stutzeri / F9-2 / 63.0* / Marine isolate
g-proteobacteria / Marinobacter sp. / 2-25 / 55.7 / Marine isolate
a-proteobacteria / Pseudomonas sp. / G-179 / 63.0* / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri 17592 / ATCC 17592 / 60.9 / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri DSM 50238 / DSM 50238 / 64.9 / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri 17594 / ATCC 17594 / 63.8 / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri 17595 / ATCC 17595 / 61.5 / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri 17587 / ATCC 17587 / 62.3 / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri CCUG 11256 / CCUG 11256 / 65 / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri 17591 / ATCC 17591 / 61.4 / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri DNSP21 / DNSP21 / 63.4 / Z.J & T.J’s collection
g-proteobacteria / P. balearica DSM 6083 / DSM 6083 / 64.4 / Z.J & T.J’s collection
g-proteobacteria / Escherichia coli / S17-1/lpir / 55.1* / Z.J & T.J’s collection
Yeast / Saccharomyces cerevisiae / Yeast Genomic DNA / Z.J & T.J’s collection
Yeast / S. cerevisiae / Yeast-mfa1 / --
Yeast / S. cerevisiae / Yeast-mfa2 / --
Yeast / S. cerevisiae / Yeast-ras1 / --
Yeast / S. cerevisiae / Yeast-act1 / --
Yeast / S. cerevisiae / Yeast-ste3 / --
g-proteobacteria / Shewanella sp. / 7-1 / 49* / Z.J & T.J’s collection
g-proteobacteria / Shewanella sp. / 7-2 / 49* / Z.J & T.J’s collection
g-proteobacteria / Shewanella gelidimarina / 11-1 / 48 / Z.J & T.J’s collection
g-proteobacteria / Shewanella sp. / 11-2 / 49* / Z.J & T.J’s collection
g-proteobacteria / Shewanella sp. / 14-2 / 49* / Z.J & T.J’s collection
g-proteobacteria / Shewanella sp. / PS-2 (SQ26) / 49* / Z.J & T.J’s collection
g-proteobacteria / Shewanella sp. / PS-3 (SQ26) / 49* / Z.J & T.J’s collection
g-proteobacteria / S. woodyi / PV-3 / 39 / Z.J & T.J’s collection
g-proteobacteria+ / Pseudomonas fluorescens+ / ATCC 17397 / 60.54 / Z.J & T.J’s collection
g-proteobacteria+ / Pseudomonas putida+ / ATCC 12633 / 63.0* / Z.J & T.J’s collection
g-proteobacteria+ / P. putida + / DSM4476 / 63.0* / Z.J & T.J’s collection
g-proteobacteria / Pseudomonas chlororaphis + / ATCC 17811 / 63.0* / Z.J & T.J’s collection
g-proteobacteria / P. fluorescens + / ATCC 17467 / 60.54 / Z.J & T.J’s collection
g-proteobacteria / P. fluorescens + / ATCC 13525 / 60.54 / Z.J & T.J’s collection
g-proteobacteria / Pseudomonas aureofacieus+ / ATCC 13985 / 63.0* / Z.J & T.J’s collection
g-proteobacteria / P. fluorescens + / ATCC 17400 / 60.54 / Z.J & T.J’s collection
g-proteobacteria / Pseudomonas aeruginosa+ / ATCC 27583 / 66.1 / Z.J & T.J’s collection
g-proteobacteria / P. auruginosa+ / ATCC 15692 / 63.0* / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri KC+ / KC / 63.0* / Z.J & T.J’s collection
g-proteobacteria / P. stutzeri+ / Tm300 / 63.0* / Z.J & T.J’s collection
g-proteobacteria / Pseudomonas mendocina + / ATCC 25411 / 63.0* / Z.J & T.J’s collection

+These strains were added for experiments further evaluating species relationships.

*Genus average.

#For phylogenetic relationships between most of the strains, please refer to the references:

(Braker, et al., 2000; Cladera, et al., 2004; Rossello, et al., 1991; Song, et al., 1999; Venkateswaran, et al., 1999; Zhou, et al., 1995)

a Data reported by Rossello (Rossello, et al., 1991);

b Data reported by Sepulveda-Torres, L. D (Sepulveda-Torres, et al., 2001), part of which was obtained by personal communication.

Figure SM 1. Phylogenetic relationship of SSU rRNA gene nucleotide sequences of part of the tested strains. The sequences were selected according to the availabilities. The dendrogram was generated by phylogenetic distance analysis with a neighbor-joining algorithm. The phylogenetic tree was linearized assuming equal evolutionary rates in all lineages (Takezaki, et al., 1995). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. Phylogenetic analyses were conducted in MEGA4 (Tamura, et al., 2007).

References

Braker G, Zhou JZ, Wu LY, Devol AH, Tiedje JM. (2000). Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific northwest marine sediment communities. Appl Environ Microbiol 66: 2096-2104.

Cladera AM, Bennasar A, Barcelo M, Lalucat J, Garcia-Valdes E. (2004). Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. J Bacteriol 186: 5239-5248.

Rossello R, Garciavaldes E, Lalucat J, Ursing J. (1991). Genotypic and Phenotypic Diversity of Pseudomonas-Stutzeri. Syst Appl Microbiol 14: 150-157.

Sepulveda-Torres LD, Zhou JZ, Guasp C, Lalucat J, Knaebel D, Plank JL, et al. (2001). Pseudomonas sp strain KC represents a new genomovar within Pseudomonas stutzeri. Int J Syst Evol Microbiol 51: 2013-2019.

Song B, Haggblom MM, Zhou JZ, Tiedje JM, Palleroni NJ. (1999). Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp nov and Azoarcus toluclasticus sp nov. Int J Syst Bacteriol 49, 1129-1140.

Takezaki N, Rzhetsky A, Nei M. (1995). Phylogenetic Test of the Molecular Clock and Linearized Trees. Mol Biol Evol 12: 823-833.

Tamura K, Dudley J, Nei M, Kumar S. (2007). MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.

Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, MacGregor BJ, et al. (1999). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49: 705-724.

Zhou JZ, Fries MR, Cheesanford JC, Tiedje JM. (1995). Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus- Tolulyticus Sp-Nov. Int J Syst Bacteriol 45: 500-506.