190 Chapter 6 stress. Not only the amount of significantly shifted proteins was notably fewer than transcripts, but the majority of the proteins remained assigned to “Ca. Methanoperedens” after 12 weeks of salinity increase (Fig. 1B and Supplementary Table 9). argG 1 glmS thrB argG 2 atoB phaC phaE 1 phaE 2 cooS 1 cooS 2 mcrD 1 mcrB mcrD 2 mcrA hydrA2 1 hdrD 1 hydrA2 2 hdrB2 1 hdrD 2 hdrB2 2 mtd hdrB2 3 norB 1 norB 2 norC nifU 1 norV nifB amt nifU 2 −6 −3 0 3 6 Aminoacid metabolism Acetate | PHA CODH MCR Methane metabolism Nitrogen metabolism pilA clpB 1 clpP 2 clpP 3 clpB 2 ftsZ 1 cdc6A p ftsZ 6 ftsZ 7 smc ftsZ 2 ftsZ 3 ftsZ 4 ftsZ 5 parA minD MEMO1 1 MEMO1 FlaI flaB FlaI TIVSS p mcp Arch fla DE Cell adhesion Cell aging Cell cycle Cell division Cell morphology Cell motility Chemotaxis ATP2C TC.KEF copB dnaJ HSP20 dnaK cct 1 cct 2 cct 3 cct 4 porB cct 5 cct 6 put trans 1 put trans 2 put trans 3 hsdS nreA put trans 4 top6B put trans 5 ligD put trans 6 ginS polB put trans. dnaG OGG1 mscL kaiC 1 kaiC 2 kaiC ferritin like AB pdtaR 1 pdtaS 1 SEC11 1 pdtaR 2 pdtaS 2 SEC11 2 ltrA RP−L14 RP−L21e RP−L15e 1 RP−L1 RP−S3Ae RP−L10 RP−L3 RP−L15e 2 RRP42 deaD phnD pstS ABC−2 ABC.CD.P 1 yebQ ABC−2.P pstC ABC.CD.P 2 Cation transporter Chaperon | Peptidase Circadian clock DNA replication repair Downshock channel Ferritin Response regulator Retron type reverse transcriptase Ribosomal protein RNA degradation Substrate transport CENTRAL METABOLISM MORPHOLOGY/ LOCOMOTION STRESS RESPONSE Log2 fold change Log2 fold change −3 0 3 2.5 0 -2.5 -5 A B C ferritin like Log2 fold change Motility machinery cell positioning Figure 4. Three-way categorization of top differentially expressed genes (P<0.05) of “Ca. Methanoperedens” between 0% to 1.5% salinities. Categories include central metabolism A, morphological change and locomotion B, and overall stress-related response. C Up- and downregulated transcripts are indicated in the y-axis for panels A and B and x-axis for panel C. Up- and downregulated genes are referred to as log2 fold change. For panels B and C, additional annotation includes a plasmid-harboring and potential phage-related transcript, FlaI_TIVSS and ltrA, respectively.
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