title: Induction of Viable but Nonculturable State in Rhodococcus and Transcriptome Analysis Using RNA-seq.
abstract: Viable but nonculturable (VBNC) bacteria, which maintain the viability with loss of culturability, universally exist in contaminated and non-contaminated environments. In this study, two strains, Rhodococcus sp. TG13 and TN3, which were isolated from PCB-contaminated sediment and non-contaminated sediment respectively, were investigated under low temperature and oligotrophic conditions. The results indicated that the two strains TG13 and TN3 could enter into the VBNC state with different incubation times, and could recover culturability by reversal of unfavourable factors and addition of resuscitation-promoting factor (Rpf), respectively. Furthermore, the gene expression variations in the VBNC response were clarified by Illumina high throughput RNA-sequencing. Genome-wide transcriptional analysis demonstrated that up-regulated genes in the VBNC cells of the strain TG13 related to protein modification, ATP accumulation and RNA polymerase, while all differentially expressed genes (DEGs) in the VBNC cells of the strain TN3 were down-regulated. However, the down-regulated genes in both the two strains mainly encoded NADH dehydrogenase subunit, catalase, oxidoreductase, which further verified that cold-induced loss of ability to defend oxidative stress may play an important role in induction of the VBNC state. This study further verified that the molecular mechanisms underlying the VBNC state varied with various bacterial species. Study on the VBNC state of non-pathogenic bacteria will provide new insights into the limitation of environmental micro-bioremediation and the cultivation of unculturable species.
authors.affiliation: Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.|Key Laboratory for Water Pollution Control and Environmental Safety in Zhejiang Province, Hangzhou 310058, China.
authors.forename: Xiaomei
authors.initials: X
authors.lastname: Su
authors.affiliation: Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.|Key Laboratory for Water Pollution Control and Environmental Safety in Zhejiang Province, Hangzhou 310058, China.
authors.forename: Li
authors.initials: L
authors.lastname: Guo
authors.affiliation: College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China.
authors.forename: Linxian
authors.initials: L
authors.lastname: Ding
authors.affiliation: School of Medicine, Stanford Universtiy, Stanford, California 94305, USA.
authors.forename: Kun
authors.initials: K
authors.lastname: Qu
authors.affiliation: Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.|Key Laboratory for Water Pollution Control and Environmental Safety in Zhejiang Province, Hangzhou 310058, China.
authors.forename: Chaofeng
authors.initials: C
authors.lastname: Shen
mesh_terms: D015536:Down-Regulation; D005798:Genes, Bacterial; D012329:RNA, Bacterial / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D012240:Rhodococcus / Q000166:cytology* / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D012329:RNA, Bacterial