Journal: Frontiers in Microbiology

Article Title: Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis

doi: 10.3389/fmicb.2020.01959

Figure Lengend Snippet: (A) Measured ammonium and nitrite levels in the K. stuttgartiensis MBR1 bioreactor and sampling times for transcriptomic analyses, indicated with vertical lines above the graph. (B) Venn diagram showing the number of genes that were exclusively expressed during either ammonium- (yellow) or nitrite-limitation (purple), and the genes that were expressed in both conditions. (C) Venn diagram showing only the genes significantly upregulated > 1.5-fold in either ammonium- (yellow) or nitrite-limitation (purple). The overlap includes all genes with either (1) very low expression levels (basemean < 4), or (2) expression levels that were within 1.5-fold change between ammonium- and nitrite limited conditions, or (3) with changes in expression levels that were below the significance level (padj > 0.05). Note that the 707 genes not expressed in either condition are not included in the Venn diagrams. (D) Bar graph of P II regulator genes (nrp1-4), ammonium transporter genes (amt1-4, amtb1-2, and amtB/1), nitrite transporter genes (focA1-5 and nar1), nitrate transporter genes (narK1-2) and their expression levels under both ammonium- (yellow) and nitrite (purple) limited growth. Statistical significance ns: * p = 0.05, ** p = 0.01, **** p = 0.0001. RPKM values corresponding to each bar are shown in .

Article Snippet: Kuenenia stuttgartiensis MBR1 was cultivated in a single cell membrane bioreactor (MBR) Applikon B.V. Schiedam, Netherlands) as described previously ( ).

Techniques: Sampling, Expressing

Journal: Frontiers in Microbiology

Article Title: Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis

doi: 10.3389/fmicb.2020.01959

Figure Lengend Snippet: Schematic representation of K. stuttgartiensis MBR1 genes that are either up- or downregulated in response to ammonium- or nitrite-limiting bioreactor growth conditions. (A) graph showing all genes as dots on vertical line, with the relative expression on the y-axis. Genes indicated in translucent blue were either not significantly expressed, or not significantly different between the two conditions. Genes indicated in purple were expressed at a significantly higher level in response to ammonium limitation compared to nitrite limitation. Genes indicated as red dots were expressed at a significantly higher level in response to nitrite limitation when compared to ammonium limitation. Circles were drawn around genes that are in very close genomic proximity. XX = KSMBR1_3177, KSMBR1_3122, and KSMBR1_3846. (B) Synteny and description of genes that were expressed at a significantly different level between nitrite- and ammonium-limiting conditions. Roman numerals I–V indicate genes that were expressed relatively more during nitrite-limiting conditions, and roman numerals VI–XII indicate genes expressed relatively more during ammonium-limiting conditions.

Article Snippet: Kuenenia stuttgartiensis MBR1 was cultivated in a single cell membrane bioreactor (MBR) Applikon B.V. Schiedam, Netherlands) as described previously ( ).

Techniques: Expressing

Journal: Frontiers in Microbiology

Article Title: Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis

doi: 10.3389/fmicb.2020.01959

Figure Lengend Snippet: A schematic overview of a K. stuttgartiensis cell and the differential expression of gene products related to metabolism and nutrient transport under nitrite- versus ammonium limited bioreactor growth conditions. Transporters have been drawn on the anammoxosome membrane for comparison but their localization on either of the three anammox membranes awaits experimental validation. Genes up-regulated under nitrite- relative to ammonium limiting conditions are indicated in purple and genes upregulated under ammonium- relative to nitrite-limiting conditions are indicated in orange. Genes that are not affected when grown under either nitrite- or ammonium-limiting conditions are indicated in green. A circle within each transport related gene indicates relative expression level. OM, outer membrane; IM, inner (cytoplasmic) membrane; AM, anammoxosome membrane; HK, histidine kinase domain. Proteins depicted in this image: Ammonium transporters: AmtB/amt1 (KSMBR1_2086), Amt_1 (KSMBR1_2627), Amt_2 (KSMBR1_2630), Amt_3 (KSMBR1_2632), Amtb_2 (KSMBR1_3866), Amtb_1 (KSMBR1_3722), Amt_4 (KSMBR1_3716); Ammonium transport P II regulators : Nrp1 (KSMBR1_2628), Nrp2 (KSMBR1_2631), Nrp3 (KSMBR1_3717), Nrp4 (KSMBR1_3718); Nitrite transporters: FocA_5 (KSMBR1_3008), Nar1 (focA_6) (KSMBR1_3009), FocA_3 (KSMBR1_1474), FocA_4 (KSMBR1_1475), FocA_2 (KSMBR1_1070), FocA_1 (KSMBR1_0300), HPP (Putative nitrite transporter, KSMBR_1075); Nitrate transporters: NarK1 (KSMBR1_3317), NarK2 (KSMBR1_3299); Anammox key metabolism: NirS (KSMBR1_0452), HZS ( hzsA : KSMBR1_2705, 2713, 3603), hzsB : (KSMBR1_2704, 2712 and 3602), and hzsC : (KSMBR1_2703, _2711, and 3601), NXR (A: KSMBR1_1455, B: 1458, and C: 1459), HAO (KSMBR1_2163), HAO r/b3 (KSMBR1_3792), HOX (KSMBR1_2670); Electron transport chain: FDH (KSMBR1_2469, 2470, 2471, 2479), r/b 1 (KSMBR1_1020 – 1021), r/b 3 (KSMBR1_ 3792 – 3797), r/b 2 (KSMBR1_1275 – 1283), ATPase (KSMBR1_0120 – 0130), NADH-DH (KSMBR1_3978 – 3990), ETM (unknown electron transport module).

Article Snippet: Kuenenia stuttgartiensis MBR1 was cultivated in a single cell membrane bioreactor (MBR) Applikon B.V. Schiedam, Netherlands) as described previously ( ).

Techniques: Quantitative Proteomics, Membrane, Comparison, Biomarker Discovery, Expressing