Induction of Viable but Nonculturable State in Rhodococcus and Transcriptome Analysis Using RNA-seq

PloS One
Xiaomei SuChaofeng Shen

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 def...Continue Reading

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Citations

Feb 1, 2019·Critical Reviews in Food Science and Nutrition·Jae-Hyun Yoon, Sun-Young Lee
Sep 10, 2020·Frontiers in Microbiology·Jessica ZampolliAlessandro Orro
Dec 16, 2020·Comprehensive Reviews in Food Science and Food Safety·Kai DongXiaojun Liao
Jan 31, 2021·Biotechnology Advances·Miroslav PátekJan Nešvera
Oct 15, 2021·Frontiers in Microbiology·Alka KumariBhavanath Jha
Oct 31, 2021·Scientific Reports·Jessica ZampolliPatrizia Di Gennaro

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Datasets Mentioned

BETA
KM235731
KP410397
SRA236830
SRA236842

Methods Mentioned

BETA
reverse transcription-PCR
RNA-Seq
flow cytometry
Illumina sequencing
PCR
environmental stresses

Software Mentioned

EBseq
BWA
featureCounts
KEGG Orthology ( KO ) system
iPath2
MEM
SPSS

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