Influence of rehydration on transcriptome during resuscitation of desiccated Pseudomonas putida KT2440

Abstract

Purpose Pseudomonas putida KT2440 is a desiccation-sensitive bacterium that loses culturability after 15 days of air desiccation. We have previously shown that P. putida KT2440 can develop a viable but nonculturable (VBNC) state after being exposed to desiccation stress and eventually recover when desiccated cells are rehydrated for at least 24 h. Methods To determine which genes of transport, oxidation-reduction, and transcription processes could be involved in the return of P. putida KT2440 to the culturable state, a transcriptome analysis was carried out comparing the gene expression of non-desiccated samples with samples subjected to desiccation followed by 20 min of rehydration or desiccation followed by 24 h of rehydration. Results Desiccation stress triggered a VBNC state of P. putida. The major response was detected after 24 h of rehydration with 148 upregulated and 42 downregulated genes. During the VBNC state, P. putida activated transmembrane transport processes like that of siderophores through a TonB-dependent transporter and putative polyhydric alcohol transport systems. Prolonged rehydration with distilled water resuscitated P. putida KT2440 cells activating the catabolism of phenylalanine/tyrosine to provide energy and carbon for ubiquinone biosynthesis while maintaining a reduced protein synthesis. On the other hand, the interruption of the TonB-dependent receptor gene (PP_1446) increased desiccation survival of the mutant strain. Conclusion The activation of the iron transport system (TonB-dependent siderophore receptor) and alcohol transport can be helping the VBNC state of P. putida. Activation of catabolism of phenylalanine/tyrosine and reduced protein synthesis was needed for resuscitation from the VBNC state.

The Viable but Non-Culturable (VBNC) State, a Poorly Explored Aspect of Beneficial Bacteria

“…Within the scant literature on beneficial bacteria, there are studies on P. putida KT2440 and C. metallidurans . Transcriptomic studies of P. putida KT2440 in the VBNC state caused by desiccation stress [ 127 ] showed that six genes related to transmembrane transport and oxidation-reduction processes were upregulated. The ethylene glycol porin (PP_2662) and substrate-binding protein (PP_2676) genes could transport and degrade polyhydric alcohols, which are accumulated during desiccation stress as compatible solutes.…”

Microbial anhydrobiosis

“…During the rehydration process, desiccated microorganisms show rapid changes in gene expression (Finn et al, 2013;Rajeev et al, 2013;López-Lara et al, 2020). For example, López-Lara et al (2020) reported that within 20 minutes of water addition, the expression of genes involved in phenylalanine/tyrosine catabolism in the Gram-negative bacterium Pseudomonas putida were strongly upregulated, providing carbon substrates for energy generation.…”

“…During the rehydration process, desiccated microorganisms show rapid changes in gene expression (Finn et al, 2013;Rajeev et al, 2013;López-Lara et al, 2020). For example, López-Lara et al (2020) reported that within 20 minutes of water addition, the expression of genes involved in phenylalanine/tyrosine catabolism in the Gram-negative bacterium Pseudomonas putida were strongly upregulated, providing carbon substrates for energy generation. In a recent metatranscriptomic study of desiccated and wetted soil microbiomes, statistically significant changes in gene upregulation (e.g., motility genes, transporter genes) and downregulation (e.g., stress-response genes, autotrophic carbon-acquisition genes) were Accepted Article observed only 10 minutes after the addition of water to desiccated soils (León-Sobrino et al, 2021).…”

“…During the rehydration process, desiccated microorganisms show rapid changes in gene expression (Finn et al ., 2013; Rajeev et al ., 2013; López‐Lara et al ., 2020). For example, López‐Lara et al .…”

“…For example, López‐Lara et al . (2020) reported that within 20 min of water addition, the expression of genes involved in phenylalanine/tyrosine catabolism in the Gram‐negative bacterium Pseudomonas putida were strongly upregulated, providing carbon substrates for energy generation. In a recent metatranscriptomic study of desiccated and wetted soil microbiomes, statistically significant changes in gene upregulation (e.g.…”