TABLE 1

Selected differentially expressed transcripts in cocultures of E. coli and R. palustris compared to monoculturesd

SpeciesGeneGene description or general roleR. palustris Nx + WT E. coliR. palustris NxΔAmtB + WT E. coliR. palustris ΔAmtB + WT E. coli
Mean fold change ± SDcFDR-adjusted P valueMean fold change ± SDFDR-adjusted P valueMean fold change ± SDFDR-adjusted P value
E. colirutAbPyrimidine degradation114.5 ± 0.00.09108.0 ± 0.00.09118.0 ± 0.10.09
rutCbPyrimidine degradation60.7 ± 0.10.0158.0 ± 0.10.0160.9 ± 0.10.01
ddpXa,bd-Ala dipeptidase58.3 ± 0.10.0159.9 ± 0.10.0150.1 ± 0.00.01
rutDbPyrimidine degradation56.9 ± 0.00.0152.9 ± 0.10.0156.6 ± 0.10.01
rutEbPyrimidine degradation48.8 ± 0.10.0144.4 ± 0.10.0148.2 ± 0.10.01
rutFbPyrimidine degradation45.2 ± 0.10.0140.3 ± 0.10.0145.5 ± 0.10.01
patAa,bPutrescine aminotransferase36.3 ± 0.10.0133.6 ± 0.10.0134.4 ± 0.00.01
argTa,bLysine/arginine/ornithine binding protein35.1 ± 0.30.0138.9 ± 0.30.0135.3 ± 0.30.01
rutGbPyrimidine degradation28.5 ± 0.00.0126.9 ± 0.00.0129.0 ± 0.10.01
ddpAa,bDipeptide binding periplasmic protein23.7 ± 0.00.0126.8 ± 0.00.0121.0 ± 0.00.01
amtBa,bAmmonium transporter21.3 ± 0.20.0225.0 ± 0.20.0124.1 ± 0.20.01
yeaGbEukaryote-like serine/threonine kinase13.6 ± 0.00.0815.2 ± 0.00.0414.5 ± 0.10.06
yeaHbUnknown12.8 ± 0.00.0614.2 ± 0.10.0514.0 ± 0.10.06
metEMethionine biosynthesis−16.2 ± 0.10.03−23.6 ± 0.60.03−22.8 ± 0.50.02
fimFFimbria regulatory protein−16.3 ± 0.00.01−18.4 ± 0.00.01−20.3 ± 0.10.01
tarMethyl-accepting chemotaxis protein II−16.3 ± 0.20.01−15.8 ± 0.20.02−15.4 ± 0.20.01
purLaPurine biosynthesis−16.8 ± 0.00.03−20.4 ± 0.10.02−18.8 ± 0.00.02
flgDFlagellar basal body rod modification−17.1 ± 0.10.02−16.9 ± 0.00.01−17.4 ± 0.10.01
ilvLaBranched-chain amino acid biosynthesis−17.4 ± 0.70.02−14.9 ± 0.40.02−14.2 ± 0.50.02
pgaBGlucosamine deacetylase−17.9 ± 0.00.02−18.8 ± 0.00.03−17.3 ± 0.00.04
ilvCaBranched-chain amino acid biosynthesis−18.0 ± 0.20.03−17.1 ± 0.20.04−17.6 ± 0.20.03
metKMethionine biosynthesis−19.2 ± 0.10.03−17.5 ± 0.10.03−17.4 ± 0.10.04
tapMethyl-accepting chemotaxis protein IV−19.7 ± 0.30.01−22.0 ± 0.20.01−22.1 ± 0.20.01
flgCFlagellar basal body rod protein−20.1 ± 0.10.05
purKaPurine biosynthesis−20.7 ± 0.10.03−25.1 ± 0.10.01−21.0 ± 0.10.03
metAMethionine biosynthesis−21.0 ± 0.10.02−20.6 ± 0.10.02−20.8 ± 0.20.02
ilvGaBranched-chain amino acid biosynthesis−22.1 ± 0.10.01−19.3 ± 0.10.03−22.1 ± 0.10.01
metFMethionine biosynthesis−23.3 ± 0.10.01−22.5 ± 0.10.01−17.6 ± 0.40.03
nadBAspartate oxidase−24.3 ± 0.00.08−29.1 ± 0.10.05−23.7 ± 0.00.07
R. palustrisRPA1206aAldehyde dehydrogenase36.0 ± 0.90.0262.4 ± 0.40.01
RPA1205aPutative alcohol dehydrogenase32.8 ± 0.50.0228.6 ± 0.40.01
RPA0538Putative porin31.6 ± 2.30.03
RPA1009aPossible cytochrome P45010.4 ± 0.80.03
RPA3101aUnknown9.4 ± 0.30.0310.3 ± 0.30.04
RPA4045aPutative amino acid ABC transport8.8 ± 0.40.02
RPA3100Unknown7.8 ± 0.20.02
RPA1010Beta-lactamase-like7.7 ± 0.40.04
RPA4020aPutative amino acid ABC transport7.7 ± 0.20.02
RPA1204Unknown7.4 ± 0.10.027.4 ± 0.10.03
RPA2376Unknown−6.9 ± 0.10.04−15.4 ± 0.20.04−9.0 ± 0.20.03
RPA2142Putative fatty acid CoA ligase−7.3 ± 0.10.03
RPA2377Unknown−8.4 ± 0.20.02−16.4 ± 0.60.05−7.3 ± 0.10.02
RPA2379Probable acetyltransferase−8.5 ± 0.30.02
RPA2390Possible rhizobactin siderophore biosynthesis−9.6 ± 0.20.06−22.8 ± 0.20.05−16.8 ± 0.50.03
RPA1260aUniversal stress protein−10.5 ± 0.00.02−7.2 ± 0.00.07
RPA2380Possible TonB-dependent iron siderophore−11.4 ± 0.60.03−17.1 ± 0.10.06−18.4 ± 0.20.01
RPA1259Putative cation-transporting P-type ATPase−11.6 ± 0.40.02−10.6 ± 0.00.06
RPA2378aPutative TonB-dependent receptor−13.1 ± 0.10.03−24.1 ± 0.30.06−17.5 ± 0.30.02
  • a Genes were also identified as differentially expressed proteins in coculture (Table 2 and supplemental material).

  • b The gene is transcriptionally activated by E. coli NtrC during nitrogen limitation.

  • c Fold change values represent means ± standard deviations. Positive values indicate that the gene was upregulated in coculture. Negative values indicate that the gene was downregulated in coculture. The initial cutoff was set to a log2 value of 2 in at least 2 of 3 biological replicates. For a complete list of all differentially regulated transcripts, see the supplemental material. Differential expression was determined with the Cufflinks tool Cuffdiff (v.2.2.0) (46).

  • d The genes shown here are directly or indirectly mentioned in the text. For a full list of differentially expressed genes, see the supplemental material.