Table 2 Selected differential gene expression changes in Sideroxydans CL21 in co-culture versus monoculture.

From: Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms

Transport/Secretion genes

Gene ID

Gene

Function

log2FC (fold change)

SidCL21_0513

exbD

Biopolymer transport protein ExbD/TolR

3.74

SidCL21_0918

lolB

Outer membrane lipoprotein component of lipoprotein transport system

2.23

SidCL21_1317

 

Efflux transport system, outer membrane factor (OMF) lipoprotein

0.65

SidCL21_0494

cusA

Cobalt-zinc-cadmium resistance protein; cation efflux system protein

0.73

SidCL21_1055

gspE

Predicted secretion system protein

−2.04

SidCL21_1061

gspF

 

−2.03

Hydrogenases

SidCL21_0646

hypA

[NiFe] hydrogenase nickel incorporation protein

1.63

SidCL21_0647

hypB

[NiFe] hydrogenase nickel incorporation-associated protein

1.84

SidCL21_0649

hypC

[NiFe] hydrogenase metallocenter assembly protein

1.42

SidCL21_0650

hypD

[NiFe] hydrogenase metallocenter assembly protein

1.41

SidCL21_0651

hypE

[NiFe] hydrogenase metallocenter assembly protein

0.91

SidCL21_0648

hypF

[NiFe] hydrogenase metallocenter assembly protein

1.56

SidCL21_0636

hyaB

Uptake [NiFe] hydrogenase, large subunit

3.10

SidCL21_0637

hyaC

Uptake [NiFe] hydrogenase, cytochrome b subunit

3.06

SidCL21_0635

hyaA

Uptake [NiFe] hydrogenase, small subunit

2.93

SidCL21_0649

hyaD

Uptake [NiFe] hydrogenase, maturation protease

2.67

SidCL21_1157

hybA

Hydrogenase-2 operon protein

3.05

SidCL21_1156

hybB

Ni/Fe-hydrogenase 2 b-type cytochrome subunit

2.99

SidCL21_1155

hybC

Ni/Fe-hydrogenase 2 large subunit

2.85

SidCL21_1158

hybO

Ni/Fe-hydrogenase 2 small subunit

2.79

Dehydrogenases

SidCL21_0230

fdsA

NAD-dependent formate dehydrogenase alpha subunit

−1.79

SidCL21_0231

fdsB

NAD-dependent formate dehydrogenase beta subunit

−3.67

SidCL21_0232

fdsG

NAD-dependent formate dehydrogenase gamma subunit

−1.68

SidCL21_0739

 

NAD(P)H dehydrogenase

−0.82

SidCL21_2320

ykgG

Predicted l-lactate dehydrogenase, hypothetical protein subunit, Iron-sulfur cluster-binding subunit

1.62

SidCL21_2321

ykgF

Predicted l-lactate dehydrogenase, iron-sulfur cluster-binding subunit

1.36

SidCL21_2319

ykgE

Predicted l-lactate dehydrogenase, Fe-S oxidoreductase subunit

1.11

Flagellar/Motility/Biofilm Formation Genes

SidCL21_3027

fliE

Flagellar hook-basal body complex protein

−0.81

SidCL21_0327

cheY

Chemotaxis regulator

−0.67

SidCL21_3038

flgD

Flagellar basal-body rod modification protein

−0.62

Extracellular Electron Transfer Pathways

SidCL21_0020

wrbA

Multimeric flavodoxin

−0.86

SidCL21_0462

 

malate:quinone oxidoreductase

2.14

SidCL21_2568

 

quinolinate synthetase (EC 2.5.1.72)

1.80

  1. Samples were collected from biological replicates at the 6 d time point. All positive changes (upregulated genes) and negative changes (downregulated genes) shown in Table 2 correspond to differential gene expression patterns in Sideroxydans sp. CL21 in co-culture in comparison to the gene expression in the monocultures. p < 0.05 was considered significant.
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