Effects of iron concentration and DFB (Desferrioxamine-B) on transcriptional profiles of an ecologically relevant marine bacterium

Abstract

Research into marine iron cycles and biogeochemistry has commonly relied on the use of chelators (including siderophores) to manipulate iron bioavailability. To test whether a commonly used chelator, desferrioxamine B (DFB) caused effects beyond changing the iron-status of cells, cultures of the environmentally relevant marine heterotrophic bacterium, Ruegeria pomeroyii, were grown in media with different concentrations of iron and/or DFB, resulting in a gradient of iron availability. To determine how cells responded, transcriptomes were generated for cells from the different treatments and analyzed to determine how cells reacted to these to perturbations. Analyses were also performed to look for cellular responses specific to the presence of DFB in the culture medium. As expected, cells experiencing different levels of iron availability had different transcriptomic profiles. While many genes related to iron acquisition were differentially expressed between treatments, there were many other genes that were also differentially expressed between different sample types, including those related to the uptake and metabolism of other metals as well as genes related to metabolism of other types of molecules like amino acids and carbohydrates. We conclude that while DFB certainly altered iron availability to cells, it also appears to have had a general effect on the homeostasis of other metals as well as influenced metabolic processes outside of metal acquisition.

Fig 1. Experimental design and sampling schematic.

Three different stock cultures were used to inoculate 4 sets of experimental flasks with varying levels of iron and/ or DFB. After incubation for 18 hours, nucleic acids were extracted, and mRNA was sequenced and analyzed.

Fig 2. Siderophore-like molecules facilitate enhanced iron uptake.

Cultures of DSS3 cells that were grown in either low or high-iron media were able to acquire iron more effectively when supplemented with SLMs than cultures of DSS3 cells that were not supplemented with SLMs.

Fig 3. Heatmap displaying the R-values (calculated in primer software package using ANOSIM program) for statistically significant (p-value <0.1) pairwise comparisons between treatments.

125 out of a total of 246 total comparisons were statistically significant at p-value < 0.1.

Fig 4. Volcano plots of transcriptomes from iron-stressed cultures compared to Fe-replete cultures.

Locus tags were included in the figure for those genes that were either directly related to metal metabolism or ranking based on Manhattan distance (see S7 Table for a list of the genes annotated in the figures).