Table 1 Selected differential gene expression changes in S. oneidensis in co-culture versus monoculture.

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

Extracellular electron transfer pathways and accessory genes

Gene ID

Gene

Function

Log2FC (fold change)

SO_0168

gspF

T2aSS secretion system inner membrane platform protein

1.18

SO_0396

frdC

Quinol-fumarate reductase menaquinol-oxidizing subunit

−2.19

SO_0397

frdC

Quinol-fumarate reductase menaquinol-oxidizing subunit

−1.02

SO_1778

mtrC

Extracellular iron oxide respiratory system surface decaheme cytochrome c component

−1.55

SO_4591

cymA

Membrane anchored tetraheme cytochrome c

−1.65

Polyamine Production/Degradation Genes

SO_1274

puuB

Gamma-glutamylputrescine oxidoreductase

2.49

SO_1275

puuC

Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

2.32

SO_1276

puuE

GABA aminotransferase PLP-dependent

1.67

SO_3030

pubA

Putrescine monooxygenase

1.11

SO_4136

speC

Ornithine decarboxylase

−1.07

ABC-type Transport System Genes

SO_0486

nosD

ABC-type copper transport system substrate-binding component

−1.05

SO_0565

znuA

ABC-type zinc uptake system substrate-binding component

1.17

SO_0566

znuB

ABC-type zinc uptake system permease component

1.20

SO_1044

artI

ABC-type arginine uptake system substrate-binding component

−1.05

SO_3714

 

ABC-type monosaccharide transport system substrate binding component

−1.11

SO_4318

aggC

Type I protein secretion system bifunctional ATPase and permease component

1.04

SO_4720

tupB

ABC-type tungstate uptake system permease component

1.55

Motility/Biofilm Formation Genes

SO_0168

gspF

T2aSS secretion system inner membrane platform protein

1.18

SO_3350

pilU

Pilus retraction ATPase

−1.45

SO_3915

cheX

Chemotaxis signal transduction system CheY dephosphorylase

−1.49

SO_4053

 

Methyl-accepting chemotaxis protein

−1.16

Hydrogenase Genes/Energy Metabolism

SO_2092

hypC

NiFe hydrogenase assembly chaperone

−1.92

SO_2093

hypB

Ni2+-binding GTPase involved in regulation of NiFe hydrogenase expression/maturation

−1.50

SO_2097

hyaC

Periplasmic [Ni-Fe] hydrogenase cytochrome b subunit

−1.04

SO_2096

hyaD

NiFe hydrogenase maturation protease

−1.28

SO_2099

hyaA

Periplasmic [Ni-Fe] hydrogenase small subunit

−1.42

  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 1 correspond to differential gene expression patterns in S. oneidensis in co-culture in comparison to the gene expression in the monocultures. p < 0.05 was considered significant.
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