Identification, characterization and molecular analysis of the viable but nonculturable Rhodococcus biphenylivorans

Xiaomei Su,Muhammad Zaffar Hashmi,Yalin Wang,Linxian Ding,Chaofeng Shen,Li Guo,Faqian Sun

doi:10.1038/srep18590

Xiaomei Su, Muhammad Zaffar Hashmi + Show 5 more

Open Access

https://doi.org/10.1038/srep18590

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Abstract

Numerous bacteria, including pollutant-degrading bacteria can enter the viable but nonculturable state (VBNC) when they encounter harsh environmental conditions. VBNC bacteria, as a vast majority of potent microbial resource can be of great significance in environmental rehabilitation. It is necessary to study the VBNC state of pollutant-degrading bacteria under various stress conditions. The aim of this study was to determine whether Rhodococcus biphenylivorans could enter the VBNC state under oligotrophic and low temperature conditions, and to examine the changes of morphology, enzymatic activity and gene expressions that might underline such state. The obtained results indicated that R. biphenylivorans TG9T could enter into the VBNC state and recover culturability under favorable environmental conditions. Results from Illumina high throughput RNA-sequencing revealed that the up-regulated genes related to ATP accumulation, protein modification, peptidoglycan biosynthesis and RNA polymerase were found in the VBNC cells, and the down-regulated genes mainly encoded hypothetical protein, membrane protein and NADH dehydrogenase subunit, which render VBNC cells more tolerant to survive under inhospitable conditions. This study provides new insights into prevention and control of the VBNC state of pollutant-degrading bacteria for their better capabilities in environmental rehabilitation.

Highlights

It is worth pointing out that viable but nonculturable state (VBNC) bacteria in the polluted environments can be of great significance in environmental rehabilitation, since VBNC bacteria represent a vast majority of potent microbial resource
We explored the uncultured or VBNC bacteria in the polychlorinated biphenyls (PCBs) contaminated environments by adding extracellular organic matter (EOM) from Micrococcus luteus[23]
We aimed to investigate whether R. biphenylivorans could enter the VBNC state under oligotrophic and low temperature conditions, and under what conditions could resuscitate the VBNC cells

Summary

Introduction

Real-time PCR-based approach was used to investigate known genes involved in response to stress-provoking conditions, while RNA transcription was employed to assess the gene expression in the VBNC state[5,17,19]. The expression of rpoS and relA genes was found relatively high in the VBNC state compared with the starved cells of Vibrio cholerae by using quantitative real-time reverse transcription PCR (Q-RT-PCR)[17]. Study on the VBNC state of R. biphenylivorans in response to various stresses will provide a new insight for assessing the derivative activity of functional bacteria in natural environments. A broader understanding of VBNC bacteria could help us reveal why highly efficient pollutant-degrading bacteria generally present lower activities in a pilot-scale environmental bioremediation. Prevention and control of VBNC bacteria are likely to be useful for improving their degradation function in a field-scale environmental bioremediation

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