Fig. 4: Volcano plots comparing transcriptomes of cells from different regions of a community or following exposure to acid or alkali.

DTM plates were inoculated with cells from liquid cultures of early procyclic forms (EATRO1125) in DTM medium. a Comparison of the roots and tips of projections. For clarity the same volcano plot is displayed twice with different transcripts annotated. Left: early procyclic form markers, such as GPEET, calflagin, hexokinase 1 and prostaglandin F synthetase are upregulated in tips. Adenylate cyclases such as ACP3, ACP5, and ACP6 are differentially expressed between tip and root. Right: glycolytic enzymes and genes involved in glucose metabolism are upregulated in tips. Far-right panel: community lift of a representative SoMo plate 7 days after inoculation stained for EP (green) and GPEET (red). Tips were isolated when projections were ≥2.5 cm in length. RNA-seq was performed in duplicate. b Pairwise comparisons of untreated communities and communities exposed to acid or alkali. Tips were isolated from projections showing a clear response to the treatment (indicated with red circles). RNA-seq was performed in triplicate. The illustrations in the left and right bottom corners of the volcano plots show SoMo communities (in black) and the samples that were collected (red circles). Analysis was done using DESeq2 bioconductor package to identify the differentially expressed genes. The package integrates Wald statistics to identify significantly regulated genes and adjustments were made for multiple comparisons with FDR/Benjamini-Hochberg⁶⁹. Source data are provided as a Source Data file.