Table 2.

Most abundant proteins detected in Methylobacterium, Sphingomonas, and Pseudomonas, respectively

Protein (DB)SY1SY2CL1aCL1bCL2ARA
Methylobacterium
Methanol DH-like XoxF (M)n.d.+++++++++++++
Fae (M,R)+++++++++++++
MucR (M)+++++++++++++
GroEL (R)+++++++++++++
Hypothetical protein (R)+++++++++++n.d.
Nucleoside-diP kinase (M)+++++++++++
Methanol DH MxaF (M,R)++++++++++n.d.
Beta-Ig-H3/fasciclin (R)+++++++++++
Cold-shock protein (M)+++++++++++
Beta-Ig-H3/fasciclin (M)++++++++++
60 kDa chaperonin (M)+++++++++n.d.
Phasin (R)++++++++++
Superoxide dismutase (M,R)++++++++++
Cold-shock protein (M,R)+++++++++
Chaperonin Cpn10 (R)++++++++++
Malyl-CoA lyase Mcl (R)+++++++++
ClpP (M)+++++++++
Surface antigen (M)n.d.++++++++
SWIB/MDM2 protein (M)n.d.++++++n.d.
Invasion associated (M)n.d.+++++++n.d.
Sphingomonas
OmpA/MotB (M)++++++++++
Succinyl-CoA ligase, α (M)++++++++++
EF-Tu (M)++++++++
OmpA/MotB (M)n.d.+++++++++
EF-Tu (M)++++++++
MotA/TolQ/ExbB (M)+n.d.++++++
TonB-dependent receptor (M)n.d.++++++
GAP dehydrogenase (M)++++++
Histone-like protein (M)n.d.+++++
OmpA/MotB (M)+++++n.d.+
Glutamine synthetase (M)+++++++
EF-G (M)++++++
Uncharacterized protein (M)n.d.++n.d.n.d.++
10 kDa chaperonin (M)++++n.d.+
Skp/OmpH (M)++++n.d.+
Uncharacterized protein (M)++n.d.+n.d.+
Membrane protein (M)+n.d.n.d.+n.d.+
TonB-dependent receptor (M)n.d.n.d.n.d.+n.d.+
TonB-dependent receptor (M)n.d.n.d.n.d.+++
TonB-dependent receptor (M)+n.d.++n.d.+
Pseudomonas
OprF (R)+++++++n.d.+++
Single-stranded binding (R)++++++n.d.+++
EF-Tu (R)+++++n.d.n.d.+
Transcript. regulator (R)+++++n.d.n.d.+
GroEL (R)++++++++
DNA-binding protein (R)++++n.d.++
Unknown function DUF883 (R)+++n.d.n.d.n.d.+
Flagellin (R)++++n.d.n.d.n.d.n.d.
OmpA (R)+++n.d.n.d.n.d.+
F0F1 ATP synthase, β (R)++++++
Succinyl-CoA synth, β (R)++n.d.+n.d.n.d.+
Peptidoglycan lipoprotein (R)+++n.d.n.d.++
Unknown function DUF883 (R)+++n.d.n.d.n.d.n.d.
Succinyl-CoA synth, α (R)++n.d.+n.d.n.d.n.d.
Chaperone Dank (R)++n.d.+n.d.n.d.n.d.
Glutamine synthetase (R)++++n.d.n.d.+
Protein P-II (R)+n.d.+n.d.n.d.+
AphC (R)+++n.d.n.d.+
F0F1 ATP synthase, α (R)+++n.d.++
Hsp20 (R)+++n.d.n.d.n.d.n.d.
  • Proteins were grouped if 90% identical over at least 40% of their length. Taxonomy (at the genus level) was inferred from the protein annotation. Ribosomal proteins are not reported here, but are listed in Table S3. Relative abundances are displayed with +, ++, and +++. DB, database. M (metagenome) and R (Refseq) indicate the database used for identification. n.d., not detected; SY1, Soybean 1; SY2, Soybean 2; CL1a, Clover 1a; CL1b, Clover 1b; CL2, Clover 2; ARA, Arabidopsis.

  • Proteins were grouped if 90% identical over at least 40% of their length. Taxonomy (at the genus level) was inferred from the protein annotation. Ribosomal proteins are not reported here, but are listed in Table S3. Relative abundances are displayed with +, ++, and +++. DB, database. M (metagenome) and R (Refseq) indicate the database used for identification. n.d., not detected; SY1, Soybean 1; SY2, Soybean 2; CL1a, Clover 1a; CL1b, Clover 1b; CL2, Clover 2; ARA, Arabidopsis.