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

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.

Transcriptomic analysis on the formation of the viable putative non-culturable state of beer-spoilage Lactobacillus acetotolerans

“…Su et al . induced the VPNC state of Rhodococcus and analyzed the transcriptome of VPNC state determining that “coenzyme binding” was the dominant up-regulated GO term in the molecular function category2728. Coupled with our results, these findings indicate that “coenzyme binding” may somehow play a role in the formation of the VPNC state in more than one species.…”

Resuscitation of viable but non‐culturable bacteria to enhance the cellulose‐degrading capability of bacterial community in composting

“…Overall, at the phylum level, the 10 isolates can be divided into three groups 1, 2 and 3 which belonged to Proteobacteria , Firmicutes and Actinobacteria respectively. Strains in group 1 belonged to Gram‐negative bacteria, which were well supported by the studies that Rpf also resuscitated and stimulated the growth of some Gram‐negative bacteria (Su et al ., ,b, ,b,c,d). In particular, ZS2R8 was closely related to uncultured bacterium clone FW2_72B () which was detected at low‐level waste site with cellulosic contaminants (Field et al ., ).…”

“…Additionally, our previous studies found that extracellular organic matter (EOM) from M . luteus containing the Rpf could stimulate and resuscitate uncultured bacteria belonging to phylum Actinobacteria (Su et al ., ,b,c,d). Therefore, the results of these cultivation studies are in line with the resuscitating and stimulating functions of Rpf on cellulose‐degrading bacteria in the compost sample.…”

“…Definitely, our understanding of the degradation of cellulosic material is still limited, because most of the microbial diversity cannot be cultivated using conventional bacteriological media and remains inaccessible (Epstein, ). As well known, numerous bacteria including pollutant‐degrading bacteria can enter into a viable but non‐culturable (VBNC) state when exposed to adverse environmental conditions (Colwell et al ., ; Oliver, ; Su et al ., ,b; Su et al ., ,b,c,d). For example, it was previously reported that a novel biphenyl‐degrading bacterium Rhodococcus biphenylivorans could enter the VBNC state under oligotrophic and low‐temperature conditions (Su et al ., ,b,c,d).…”

“…As well known, numerous bacteria including pollutant‐degrading bacteria can enter into a viable but non‐culturable (VBNC) state when exposed to adverse environmental conditions (Colwell et al ., ; Oliver, ; Su et al ., ,b; Su et al ., ,b,c,d). For example, it was previously reported that a novel biphenyl‐degrading bacterium Rhodococcus biphenylivorans could enter the VBNC state under oligotrophic and low‐temperature conditions (Su et al ., ,b,c,d). Most investigators believe the VBNC state is a survival strategy which contributes to long‐term maintenance of cells viability (Keep et al ., ; Oliver, ).…”