Lab vs Soil: The Transcriptome of Pseudomonas putida

Voltmer, Stokley

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Lab vs Soil: The Transcriptome of Pseudomonas putida

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Pseudomonas putida is a candidate for use in the soil environment, in bioremediation and as a part of the soil microbiome. However, P. putida often does not behave in the lab as it does in the field. This work aims to bridge the gap between the lab and field by observing the gene expression of Pseudomonas putida grown under lab conditions (Luria broth, LB) and a soil analog (soil extracted soluble organic matter, SESOM) created by our laboratory to determine changes in gene expression of P. putida between conditions, as well as the practicality of SESOM as a soil analog. Additionally, this work examines the use of Nanopore sequencing as an alternative to traditional sequencing methods for transcriptomics. The differential expression of mRNA in P. putida grown in LB and SESOM were determined using both Illumina and direct RNA Nanopore sequencing. We found a clear difference in expression between P. putida grown in the lab and soil conditions, opening the door for further research into the underlying mechanisms of transcriptional regulation under LB and SESOM conditions. Additionally, we found that Nanopore is not a suitable method for direct RNA sequencing in prokaryotes, however this may change as the technology matures. This research will ultimately improve our ability to engineer P. putida for future soil biosensing and bioremediation applications.

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